I have to say it was in Witcher 1, when you work together with Raimund the private detective in Wyzima and at some point you are about to find out, that the one you were working with got substituted by your worst enemy in this game and only clues gave you a hint, what actually was going on!

The Dartmoor Manor level in Hitman 3.

Most memorable criminal case, for me, is the Neuhof slaughter from Kingdom Come: Deliverance, which ends up taking you all across the map to solve it. A very complicated case, you know, a lotta ins, lotta outs, lotta what-have-yous. And, uh, lotta strands to keep in my head, man. Lotta strands in old Duder's head.

Piecing together who you are and how you're used as a weapon by Atlas (who is really Frank Fontaine) to kill Andrew Ryan (who ends up being the player character Jack's father) at the end of the first Bioshock. A man chooses, a slave obeys. Would you kindly...

The Clown-bombing/Assassinations in 'Broken Sword - The shadow of the Templars'.
One of the first PC games I ever played.
Needed a whole summer in the pre-internet 90s.

The "Perfect Crime" mission from Batman: Arkham Knight. Many scene were disturbing and horryfying. But it really felt like you're a normal detective instead of detective as batman. I really enjoyed that mission

Solve Jake's murder in divinity original sin

Metal gear solid: vr missions - murder mysteries.
I mean, what could be more memorable than having to find out who broke the security camera?

My most memorable was the Batman: Arkham Origins murder case of Black Mask's girlfriend. You enter with almost no information but step by step you go from having some suspects like The Penguin, that seems likely, but later with the evidence, you deduce that it's not him. One of the most memorable parts is the twist at the end that the majority of Batman fans see coming but I have heard that a lot of people did not and were surprised.

It's got to be the murder in Delphine's "Cruise for a Corpse." After navigating through a multitude of false leads including bracelets locked in rolltop desks and casino equipment hidden in the suitcase of a priest, I finally found my way to a solution which included stolen identities, poisoned medicine and a creepy puppet stored in a secret room. The great thing in that game, though, was the ability to accuse any of the suspects of the murder. It led to at least one great ending cutscene where I accused the nicest person in the game with no evidence whatsoever and saw him led away pleading his innocence. Good times!

That's easy, the Voodoo murders from Gabriel Knight 1 :D

You actually investigate what happened and why and you get to learn about curious real life stuff too about voodoo and New Orleans. And you actually have to use that magnifying glass like a realio dealio detective lol :D! The same goes for the other two Gabriel Knight games too since the creators' of the series did a whole lot of research into the related topics when making the games.

Paradise Killer is also good, but weird :D

Oh god ufff the best crime was the one in Wolf among us. I mean, I looked for a murderer, in a world where everyone uses glamour to change their forms. You have to pretty much understand those fables involved which are in place, for example, Nerissa, the "little mermaid" to help you understand their personality.

How are fables doing in their new life? how much corruption is out there? Who will be your trusty friend? are women in dispair really in danger or plotting against their boss?

a) Women trying to fight the "crooked man" for their liberty, now... how? What happened wrong?

b) Or women trying to soft their work blackmailing their boss? what happened if that went wrong and got two of them killed?

Who really died? Nerissa glamoured as Faith? or Faith glamoured as Nerissa? are those chances even possible?

Did we really solve the mystery at all? Are you satisfied with your journey? I don't know, my lips are sealed. Also, Bigby is not as bad as people think he is.

The most memorable case I ever solved in a video game was when I realized my packrat habits in Icewind Dale 2 had actually made me guilty of criminal body disposal. You think it's perfectly normal to just pick up everything that isn't nailed down - after all, you never know what some "items" might still be good for later in the game, right? -, and suddenly even fiends from the Lower Planes call me a creepy psycho and run away, just because I casually mentioned what I was carrying around in that sack. That's when I had to confess I have a problem. ;)

Pretty neat easter egg. :D

The Case of the Disappeared Donkey Tiger said "Whoops".

"Telling this story, my dear reader, will tax me greatly" begins Dandelion in his remarkable Journal Entry, in 'Carnal Sins'. What grieves the minstrel is undoubtedly one of the most thrilling killing mysteries in 'The Witcher III', when Priscilla has been attacked leading Geralt to exciting trip through the sewers to a secret way into the morgue of Novigrad, and to works of investigation that maybe only Batman would do. A cruel and unique serial killer, making victims through the city, leaving messages and signs on every new body, and seaming to be one step ahead of his pursuer, everytime. 'The Witcher' steady pace and uncomparable narrative garanties the player's full immersion throughout the mystery, solved with wits and action, and ended with an memorable battle with a disguised Higher Vampire with a twisted and fanatical mind. Truly awesome!