Only ranking anime cases. (I read plenty of the manga but a lot of it is still untranslated). I'm also only taking into account the anime and not the manga (in case there are differences). This contains SPOILERS of tricks, murderers and everything else.
The short cases are usually in the Decent category because it's easy the entertain for one episode, but you won't get great tricks, developped characters, legends or eery backstories for most of those cases. On the other end, it's also harder to be boring in a single episode. If a short case is not in Decent, it's because it's either better than the usual short case or worse.
As always, it's subjective. From top to bottom (and with some comments) :
Great
Snow Yaksha Legend Murder => This is actually the case that made me discover Kindaichi. I might be biaised for it but I like the setting a lot. The trick require some very specific knowledge but works pretty well, there is the rivalry between Akechi and Kindaichi, false solutions, a scapegoat. This case is also Reika's beginning.
Black Magic Murder Case => This is a great case with an intriging atmosphere, good tricks and a surprising culprits.
Murder Committed by Inspector Kenmochi => A pretty good case. You know Kenmochi can't be the culprit and yet it's done well and almost make you doubt. Parts that seem weird like Busujima always surviving the attacks make perfect sense in the end and the case wraps up nicely. Tamaki is also very annoying and possibly one of the least sympathic victim in the entire serie (at least even if they are evil, many victims at least pretend to be nice to random people, not him), so seeing him blow up is a good point too.
Wax Doll Castle Murder Case => I like everything about this case, the tricks, the setting, the clue. The beginning is also funny with the fake murder case and people discussing the dying message.
Hida's Trick of House Murder Case => A good setting and great tricks make for a great case. The ending is a bit overdramatic but fits the theme of the family issues quite nicely.
Opera House Murder Case => Once again, good settings, interesting tricks.Not much to say it's a "standard" great case, if there was a blueprints to such thing.
Reika Hayami Kidnapping Murder Case => This case shows you do not need a lot of tricks or murders to make a great case. This case is about a single murder that uses a single trick, with no ancient legend or serie of murders, but that one trick and murder are very good and manage to carry the case.
Russian Dolls Murder Case => A pretty interesting case with a good atmosphere, several tricks and riddles (the location of the will) and even Takato to liven things up. The ending is also quite surprising, with both the culprit just killing for money rather than revenge and the owner of the mansion expecting things to end this way and wanting the victims to die for petty reasons. This is a surprisingly dark ending turn for a case which doesn't involve misunderstandings.
Murder in the Forest of the Demon Dog => A great case with a nice setting. It's obvious that Cerberus doesn't exist, but there is sufficient evidence planted pointing to it's existence it almost feel like it could. It's also one of the best use of the "The culprit pretend to be attacked" case since this time, the culprit does get bitten by a dog and they cannot know he doesn't actually have rabbies.
Will O' Wisp Island Murder Case => Another case with a great atmosphere and great tricks. The moment where they look into the room to see the "ghost" and the will of wisp by the window is quite creepy. The faked death is also well pulled off with several clues pointing to it.
Alchemy Murder Case => The first great case of the Returns serie. Interesting tricks and I liked the period table explaining the weird room numbers. The giant sword being a distraction was also a fun part.
Rosenkreuz Mansion Murder Case => This case feels like it's somewhat overrated to me. That doesn't mean it's not one of the best case of Kindaichi, but from what I heard about it before watching it, I expected it to be among in the Top 3 and it's not quite there. That being said, the tricks are nice and interesting, the presence of Takato and his interections with Kindaichi are amazing and the setting is good. All in all, it's still a great Kindaichi case.
Demon Killer of Silver Screen => An great case. I especially liked how the killer's theme Scorpio turned out to be an integral part of the final Double Locked Room trick.
Magical Express Murder Case => A pretty good case. The mystery of the body disappearing from the train has a pretty complete solution (my translation didn't explain it too well though, which lead to me having to check the manga to be sure of how it was done). As for why it's quite low in the great case list, it's because of the entire luring Kindaichi into the swamp plot (probably his luckiest escape yet). There is also Kindaichi accidentally breaking the bridge, which looks like it will matter but don't actually end up mattering. Still, those are small issues in a very good case.
Thunder Festival Murder Case => This case is fun. Like Reika Hayama Kidnapping , it's based on a single murder. This time, the trick isn't as impressive or complicated. However, there is a double framing and the classic family issues complicating things, But this case is more about the story of Shigure than about the crime and it does that well too. Also first (and only ?) case where the murderer isn't caught ! (Her mom talk after her death but this doesn't really count).
Good
School's Seven Mysteries Murder Case => Good introduction to the serie, interesting trick and setting. The backstory with the hidden corpses is a bit convoluted but this doesn't affect the whole case.
Bizarre Circus Murder => I really liked the atmosphere of this case with everything trying to show only a giant could have committed the crimes. The ending with Monster turned out a live is a bit of a Deus Ex Machina but then I remembered at the beginning that Akechi was called to see a patient who had just recovered from fire wounds so it was a least well foreshadowed. The trick in the burning room was quite good too.
Izumo Myth Murder Case => A case with a pretty good setting and side story. The tricks are also quite well done (even if the last trick more or less make the culprit obvious). Still well done that they manage to make us think everyone is there at a certain point while the culprit already left to kill the first victim.
Tarot Mountain Hut Murder => Like French Silver Coin, this is another case where there is a mastermind manipulating a pawn into commiting murder for them. I find this one better than the previous one with a better trick a better environment and a more interesting theme to the murders. (It was funny the Tarot themed culprit didn't know a thing about Tarot and got caught because of that).
Snow Goblin Legend Murder Case => I shouldn't be ranking this case that high. I like it a lot and the atmosphere when finding the empty hut the first day is pretty good. But seriously, no one that worked there noticed a building going missing ? So yeah, a good case in story and plot, but I'm not convinced about that entire building sinking trick. I might have ranked this case as great if the first crime trick was different (and less over the top)
Jail Gate Cram School Murder Case => I like this case, it has a real "what is happening" feel to it when you have the timestamp appearing everytimes you chance scene. There is also the suspense when you see the victims leave the rooms and suddenly cut to another scene (for a while, I thought they were killed by hidden poisoned needles like the first victim and the bodies hidden later). The entire themed murder to hide the mistake with the water was also brilliant. That being said, it's still a case mostly reliant on the area architecture and I think Snow Demon and Wax Castle did it better.
Western-style Hotel Murder Case => A good case. Some minor default is the fact that Saki somehow survive (his death in the manga makes more sense considering what happened). It's also curious Mako acts as if she knows something is going to happen but she was not involved in the murders at all.
Demon God Site Murder Case => A fun case with plenty of mysteries : the location of the treasure, the locked room murder, the identity of Satsuki's mother. It also had a decent setting with the cursed items being involved in the murders. The ending has a convenient amnesia though (and it's quite unlucky that the bell happened to crush someone, leanding to the Bell death being fulfilled as well). Still, an enjoyable case.
Opera House The Last Murder => Another case happening in the cursed Uta Island. This one also had a chandellier dropped by a trick with a complicated wire setup. I don't think it was as good as the first Opera House case but it's not bad at all.
Drifting Firefox Murder Case => A case similar to Yukikage Village Case. I liked this one better. The theme is similar but I like how for a while, there is a sub mystery as to how the school trip could possibly be the motive since nothing bad happened. (not the beeeeees !). The tricks are mostly fine (and I liked them more than the Yukikage case). The entire legend being used as a decoy is fun too. That being said, making the masked victim look like she was alive was one of the most obvious trick ever and the instant I saw her, I knew she was dead and this was some kind of alibi setup.
Ghost School Murder Case => A case based mostly on it's creepy atmosphere. It has a single murder with a trick that's not too complicated. Despite this , it manages to stay interesting it's entire length. This is also another of the few case with supernatural elements.
Chidamari's Room Murder Case => A rather unusual sized case (it's either 1 or 3+ episodes). It has a decent atmosphere and I liked the Go theme. The trick isn't that complex but for a short case I will forgive it. I don't have anything bad to say about this case
Young Kindaichi's Trip of Death Preparedness => The atmosphere of the case is pretty fun, with Kindaichi doubting himself and wondering if Takato managed to hypnotize him. The case is quite servicable in general however there are a few things that prevent it from ranking any higher. First, while it does make some sense, the killer keeping a child like appearance is pretty convenient (and I'd almost say unfair). Another thing is the killer messing up so that Akechi doesn't die. Of course, the author couldn't actually kill Akechi but the story has the contrive a reason as to why he was stabbed the wrong way. It might have been better to show a different victim actually been killed. THis is also sort of recycling the "The killer was with Kindaichi all along and that's how he could always arrange things" plot from Kindaichi the Kiler. Still good, but those points drag down the case a bit.
Broken Heart Lake Legend Murder Case => I didn't like the setting too much but the tricks with the fake death and fake message were good. The clues were decent too.
Ghost Passenger Ship Murder Case => A case with quite an eery beginning (with the nightmare, the rumors, the empty room of the captain). While the solution isn't that complicated and the motivation quite standard (though a nice throwback to the Broken Heart case), this is a solid case.
Young Akechi's Splendid Challenge => A short case focused on Akechi's first case.
Shanghai Mermaid Legend Murder Case => A good case. The twist that the first death was actually a suicide is pretty good (though most of the Kindaichi killers plans are planned well in advance, so the culprit must have been a pretty quick thinker to come up with it just from the suicide). A thing that annoyed me a bit was the police never believing Kindaichi which happens every time the inspector in charge is not Akechi or Kenmochi. It was fine one or twice, but by that point, we have seen it many times.
Yukikage Village Murder Case => A case more on the emotional side than the mystery side. It accomplishes this quite well, while also having a decent mystery with the snowprints. It's not the most complex case, but it doesn't need to be as it's not it's main goal.
Murder in Mirror Labyrinth => A short one episode case. However, I like it more than the usual one parters. Nothing too special but I found it fun how the labyrinth being cheap allowed to pull that trick off.
French Silver Coin Murder Case => I like how this case worked but I do feel like it was based on a lot of luck from the culprit. The victim drinking the poisoned wine in the second murder, Masumi recognizing the perfume sent and deciding to shot Yurie, the entire plot with Hiroshi to control Masumi. The murder plan was good, but it seems very lucky to have worked so well (even though Yurie surviving was still an issue that ended up ruining it)
Campsite's Mysterious Case => A pretty funny short flashback story explaining while an owl is judging Kindaichi.
Young Akechi's Splendid Sword => Another case about Akechi's past. It seems to have an obvious solution (icicle) but it's a bit more complicated than that. The motive about the culprit being jealous of someone who was not going to catch up to him was also quite different from the usual revenge motives.
Murder in Valentine Eve => A good shorter case. It doesn't do anything special and the tricks aren't that new (one of them is another "Trick the victim to say the wrong location) but it's enjoyable.
Midsummer's Nightmare Murder Case = This is a weird short case. It's mostly based on a contrived dying message which usually wouldn't rank that high but it's so weird compared to the rest it's memorable. This is also one of the few case dealing with the supernatural.
Murder at 10.000 Meter Altitude => A good short case with Kindaichi and Akechi working together to solve a murder in a plane. The case itself is solid but the copilot being involved is sadly a bit too obvious the "captain" is a fake during the smoke part when you see he hides his face and wear sunglasses. It's not the entire solution but this is still a bit glaring.
Superintendent Akechi's Splendid Inference => A short case. It's a bit more involved than the standard short case with alibis , testimonies and timeframe. It's still not that complicated but it's good for it's size. It's also quite fun to see Kindaichi in jail !
Average/Decent
Young Akechi's Splendid Concerto => A short case with Akechi. The mystery isn't too complicated but the story of the group that hate each other and how it turned out was quite good.
Superintendent Akechi's Splendid Inference in Las Vegas => Another case focused on Akechi. Unlike most Kindaichi cases, you know who is the culprit from the beginning. Akechi also suspects the culprits for a while leading to some interesting dialogues between. It's another rare case where the motive is money. I do wonder how plausible the trick is for that one though. No matter how much better of a player Goldman was, could he really ensure that every moves done was the same ? If the bad players made any blunder and not followed the gameplan, it would have ruined everything.
Evil Spirit of the Diving Pool => A short case with an unusual trick.
Half Murderer => A good short case. It's is quite unlike the other cases in that you know what the culprit look like. Unfortunately, there are twins. What I like about this case is how it starts with the culprit having taken confusing actions,but they are all explained in the end.
Murder Restaurant => It's not really a normal Kindaichi case, more like a funny side story from the point of view of a murderer. Still, it's not bad and does it job well.
Mystery of Missing Gold Medal => Yet another case where the Gentleman Thief get framed. I liked this one more than the others two, despite it being a short case. The trick is decent for such a short case and the story is tight and compact. It doesn't do anything amazing but it doesn't mess up either.
Killing Poker => A short case focusing a Akechi. Decent enough.
Murder by Gentleman Thief => This case is muddied up too much by the presence of both the Gentleman Thief and the Culprit. There is no special setting or legend about this case, the tricks are not very impressive (tricking the victim to make him say he is in the wrong place, faking an attack). This case isn't bad but it's very average.
Gunshot at 04:40 a.m => As a short case I can forgive a lot and the entire thing mostly work. Still, I feel like it could have be better without making the suicide motive so complex "She wants to frame him for her death, but she actually still want to it to be found out she was framing him". Using the train as part of the trick was a good idea though.
Devil Suite Murder Case => This case is so average I don't remember much about it, neither in good or in bad. But I do remember it had an interesting setting with the song but that it also had the classical trick of the culprit faking being attacked.
Sorrowed Ghost Legend Murder Case => This is an average case. I don't have too much to say about it, whether bad or good.
Murderous Intention Under Freezing 15 Degrees => It's a nice short case.
Reika Hayami and The Uninvited Guest => A culprit PoV case very similar to Murder Restaurant. I think Murder Restaurant is funnier.
Murder in the Bloody Poll => A short case where Miyuki is framed.
Kindaichi Fumi's Pretty Activity: Ukai Village Murder Case => A short case with Fumi as the main character. It's not very developped but the ending with her teacher turning out to be the culprit instead of one of the suspects is quite surprising.
Young Boy's Retaliation => A bit of a weird case to pick for a special. It's also one of the rare non murder Kindaichi case and ALSO an Akechi case. In that case, the mysteries aren't really that complex and it's mostly about the character interactions. Finally, it ends in a cliche happy ending. None of that case is bad but it does feel a bit boring and you don't learn that much more on Akechi that you knew before.
Kindaichi Fumi's Pretty Activity: Fumi's Kidnapping Case => A decent short case. Not much more to say about it really.
The Demon Loses His Way => Thie short case in which technically nothing happen ! But Akechi left Kindaichi a story about a mystery. Outside of the original presentation of the case, there is nothing special about this case.
Who Killed the Goddess? => A short case. It is simple but works well enough.
Kindaichi Fumi's Pretty Activity: Ransom Disappears in The Snows => A short case about a kidnapping instead of a mruder. It's nothing too special.
Mystery of Instant Disappearance => Another watchable short case. Nothing bad to say about it, but not much good either.
Challenge from the Gentleman Thief => A forgettable short case. Once again, mixing both the Gentleman Thief and a killer doesn't turn out too well.
Bad
Alibi in The Film => A forgettable short case. While it does have Miyuki being hurt, this was pulled out far better in School's Seven Mysteries Murder.
Female Doctor's Bizarre Plot => This case is pretty much another instance of Murder Restuarant and Reika Hayami and The Uninvited Guest. Unfortunately, this one is the worst of the three. It's not really funny and the ways she messed up aren't especially interesting.
Accomplice X => A forgettable short case. From what I recall, the culprit got caught because only a teacher could have written the messages on the desk and because he probably erased his fingerprints. This isn't exactly solid proof and there is also the question of why he would take the risk to kidnap a student to trick another into murdering someone. ( since he left his victim alive, this was even riskier than him doing the murder himself).
Death God Hospital Murder Case => A rather forgettable case. The fact the culprit was in the room and only escaped because people thought it was a picture instead of a mirror doesn't help it's case either.
Murder Committed by Young Kindaichi => The actual trick of the first murder is good. However, all the other murders are basically throw away to frame Kindaichi, but while it's explained how the culprit could know when to be there, it's never explained how he managed to always get into the position to kill the victims without being spotted by anyone (especially when it's at the TV Station). All is not bad in that case, as it shows Akechi does trust Kindaichi and the message actually made sense even translated.
Computer Mountain Hut Murder Case => I'm quite confused about what happened in that case. I even checked both a French and an English translation and they were both unclear about what happen. The tricks seemed complex and involved Time and Names but it must have been needlessly confusing if after pausing and rewatching several times the explanations, I was still unsure about the details.
Vampire Legend Murder => This case have a decent atmosphere, but I didn't like it a lot. The first trick was quite standard (making a room look like another) and the second trick rely on the most sensitive elevator in the world. While I suppose it's not impossible, I don't find it really convincing. The motive and the backstory weren't very interesting either.
Treasure Island Murder Case => This case encounters a classic issue with japanese hidden code : it doesn't make much sense when translated. This ruined the treasure hunt part for me. Another issue is that the answer feel underwhelming : there is an entire island and plenty of Tori gates, but only one end up being relevant. There is also the child, whose only goal seems to be a blatant red herring. The tricks themselves are actually decent but can't support the case.
House of Games Murder Case => The idea being that case is pretty good : a psycho is supposedly organizing a death game, however it's just a cover to hide the fact he has specific targets he wants dead in order to gain money. Unfortunately, the actual realisation of the idea is a bit lackluster. Even with the multiple possible ways to kill the targets, this felt easily reliant on luck. The tricks themselves aren't anything special and you have to wonder how Kindaichi survived the room on fire.
Massacre of Deep Blue => I'm not sure why they made a movie at roughly the same time with a changed story. Anyways, the anime version of this case is quite mediocre. First, it's very long and about half of it is like a pseudo action movie rather than a mystery. It also has some really exagerated plot points like the elevator handling several people but not able to lift a gun with them (another very specific elevator like in Vampire Legend I see !). It's a large change to the usual formula, and not a successful one.
Graveyard Island Murder Case => This case has a plan reliant on luck like French Silver Coin Murder Case but even more. There are many ways the whole plan involving the "Ghost soldier" could have handed badly. Even if he couldn't clearly see and couldn't talk, he could have fallen and been caught,which would have ruined the plan. If he hadn't eaten a bread or had eaten it at the wrong time, he wouldn't have died or would have died at an inconvenient moment. While the explanation made sense as to why it happened like that, you could imagine many many ways it would have turned out differently, and I don't think the culprit could have expected it to turn out this well. Another "issue" is the presence of an accomplice which cheapen the case (accomplice make things much easier). I find this case highly questionnable but it didn't annoy me like the cases in the Terrible category so I'm putting it bottom of Bad.
Terrible
Amakusa Treasure Legend Murder Case => I have several problems with this case. First, it's suffer from the meaningless deaths syndroms : deaths that happen and are quickly forgotten, because they aren't relevant in either the mystery or for the characters. The main trick is also not very impressive (tricking the victim to take a longer path). This is also a five episode cases which highlight it's bad points even more. Also, the final reveal that the money wasn't even available in the end seems a bit gratuitous (if the culprit did that much research, surely he would know about the financial situation of the director, he didn't do bankrupt in one day). Creating an entire folklore and rumor in a few months seems hightly dubious too. Finally, there is also something weird about Kindaichi finding the treasure and still having money issue later on. Even if he gave a bit for the girl's hospital costs, this couldn't be nearly enough to be the full treasure.
Black Butterfly of Death Murder Case => I really don't like this case. First, only Ruri's murder seems to have any trick to it, the other murders or attempt don't end up warranting any investigation. Second, even Ruri's murder is not that interesting and very simple. In fact I think I can spoil the entire case with 3 words "Body under butterflies" , which I don't think can be done for a lot of cases. Kindaichi has a lot of dramatic endings where the culprit understand he shouldn't have done it after a dramatic reveal but this might be the most overdramatic and contrived reveal in all of Kindaichi. Finally, there is the random addition of Eiji (due a convenient butterfly shaped scar) with a convenient amnesia. There is also the fact nobody seemed to have noticed the Black Butterfly of Death were the same as the Blue butterfly, which seems weird considering every expert gathered at that mansion.
Kowloon Hong Kong Treasure Murder Case => This is probably my most hated case of Kindaichi. While Black Butterfly is boring, it's not as annoying to me as Kowloon Hong Kong. What I find bad in it : The way the corpse get into the hotel, while not quite the same, it reminded me off the Pendulum corpse of Ace Attorney, which is pretty bad, The culprit looking exactly like Miyuki being an integral plot point and part of the trick. The suitcase containing a non nuclear explosive that can destroy a city (even Nuclear it would be a hard sell considering the size of the thing so non Nuclear is impossible). The fact the culprit paid someone to help ensure the first victim drank the poison, sure they might have planned to kill them later but it's far from reliable and could have resulted in them being exposed had the second victim thought about it for a few minutes about how suspicious this was. The foreshadowing of the poisoning trick is the most obvious ever after having the victim get super angry about a butterfly than die poisoned a few minutes after with plates having either snails or butterfly drawings. So yeah, I find plenty of wrong with this case