Honestly, this horror games thing (I'm writing a Halloween special) has very much been a personal journey of "your faves are problematic". (And these are all personal faves, I'm not just knocking them for their own sake.)
Blood Omen: The Legacy of Kain was going to be here but is no longer even on my list (because I can't currently stand to look at it due to this mess https://eldritch.cafe/@HauntedOwlbear/112568940656212305)
GK1 has some... interesting ideas about voodoo. The factual research is pretty solid, but Tetelo is a giant fucking problem that reveals that maybe the white lady who'd never been to New Orleans was not the person to tell a story about voodoo, ancestry and the legacy of slavery. There was a lot of this kind of thing in the 90s.
Phantasmagoria isn't something I'm personally attached to from the past, but it has the whole s-word disability slur issue that's causing me trouble. It's probably going in all the same, with about a million content warnings. I mentioned to someone else that the rape, misogyny and fatphobia were at least expected.
I Have No Mouth... covers a lot of difficult territory, especially regarding Nimdok, and I think we can thank Ellison's very direct personal involvement in the game's writing for the good handling of that one.
I lowkey suspect that Ellen and Benny's character alterations were made to make them more palatable to family audiences - EVEN THOUGH the game was very much for adults. While Ellen's changes could be arguably meshed into the original story, Benny's been more extensively reworked in a very 90s "we don't talk about the gays even if they're terrible people" kind of way.