The Suffering was dark, but still a bit too shallow. It had potential, though, and it certainly wasn't a trot through happy land. Actually, it was probably darker than a lot of horror games on certain levels.
Also Pug, Blood Omen was a PC game. It was also on PS1.
As for Alice... I'm probably the game's biggest fan, like, ever, but I don't know how dark I'd say it was. Again, I think that's probably because the artistry was just so heavy, for me that took precedence over most everything else. Not to mention the theme of the game was really pretty positive in the end.