For me it’s games that force you into a position where you end up being morally/emotionally punished for the actions taken. Especially in games where your character has no identity beyond the actions you’ve taken.
I know this is an old thing, especially in the Final Fantasy series: FF2/4 had Cecil and his destruction of Mist Village (Which in the original english version had the player delivering a ‘Package’ to the village, though in the Japanese version it was ‘bomb’. There were Bowlderization issues there!) and then FF3/6 had the whole thing with Terra invading that city with the Magitech troopers. However, these both had character development outside of that and you knew why the player ended up playing though those sections.
Shadow of the Colossus had something of this in it, not that I minded because it was really a pseudo-story game anyway.
I’ve seen a couple of flash games do that where the story is accomplishing these semi-evil acts just because you were asked, then you’re morally punished at the end (I can’t remember the name of the one I’m thinking about, but it was basically that the PC ends up being asked by a wise man to get some items from the guardians of the world, and at the end you’re basically told “Asshole, you just slaughtered the guardians just because this old man wants you to do something? What’s wrong with you!”)