I’ll start. Raven of the Inner Palace, partially because its OP is MYSTERIOUS by QUEEN BEE.
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I’m not entirely sure I understand the question being asked, but I want to say that the first season of Higurashi No Naka Koro Ni (AKA When They Cry AKA When Cicadas Cry) perfectly sets the tone and pacing of a mystery thriller where every answer the viewer gets to their questions comes with two or three NEW questions until you’re left with more questions than answers by the end of that first season.
That said, I have to cop to the aggressive animé-ness of the show, from dressing up its underage cast in fanservice-y clothing to the extreme mood whiplash between arcs, not to mention the entire weird premise (which I can’t really blurt out without major spoilers). Also large portions of the second season are dedicated to actions which I do not understand. My point is, it kinda fumbles in places.
Monogatari series, especially when you get to Owarimonogatari. A few years ago I put together a custom watch order for the series here to increase the mystery. I’m biased but I highly recommend it; there’s one or two parts that might seem a little awkward, but I think it’s overall a big improvement.
The Tatami Galaxy. The overall plot is probably pretty obvious after the first couple episodes but connecting all the details is really interesting and not something you’d necessarily pick up on the first time you watch it.
Higueashi no Naku Koro ni is similar. You figure out pretty early how the show is structured, but finding out the details is where it gets interesting.
Monster. It’s about a doctor who is accused of murder and is on the run trying to find the real culprit. He stumbles upon something that’s far bigger than he could have imagined.
It sounds like Dr. Kimble, but it’s completely different. A classic! And really really good!
Can’t say I’ve seen a ton of mystery anime, but ODDTAXI was really really good.
I’ll nominate Shadows House, although it certainly isn’t a traditional mystery.
I super liked Another. I watched it recently and was very quickly drawn in! I feel like it did a super great job presenting presenting multiple moments that built upon the overarching mystery while also creating new ones.
Try Shiki. It’s written by the spouse of the author of Another; you might find it interesting to compare their styles.
Dusk Maiden of Amnesia
Summertime rendering & subete ga f ni naru come to mind
Tell me what happened in Aragne and Feast of Amrita, it’s a mystery
