Those freaky Silent Hill nurses with their butcher knives and their jerky motions in the dark hallways with the walls plastered with dry blood and guts. When I first played Silent Hill, some of the levels brought on claustrophobia and I had to stop playing for days before I could continue. Yeah, it was pretty disturbing for me back then.

Uhm... For me it is properly Sanitarium. Due to my profound interest for dream interpretation, I couldent help but to constantly overstrain myself, trying to decipher the enigmatic nature of the story, which was spooky beyond measure. Attempting to unravel this psychotic nightmare for days, also left me somewhat ungrounded... Im glad it was only a 20 hour game, had it been twice as long I would properly have ended up in a bin somewhere.

Also, the broodmother quest in DA 1? Just as terrifying as seeing the clown from "It" for the very first time.(In television, that is. A real life encounter would be scarier than anything fiction could provide.)

What an utterly magnificent game. And yes, a considerable portion of it is disturbing as well.

Also, Time Fuck (let's just call it that). It's just a flash game, but what a flash game it is.

ah, yes... The Path :) not sure if it's even a game, but it's definitely what you're looking for :D
http://tale-of-tales.com/ThePath/

Bioshock, Dead Space, Penumbra Overture, Manhunt.

While I can't claim to have played it, Littlest Pet Shop creeps me out far more than any of the games I have played, and that's just the cover art.

Far Cry 2, the main caracter was inmoral and even... disgusing.

I have to say manhunt and such splatter things are just to violent to really be shocking, that's also the reason why resident evil went down the drain. I remember resident evil 1 was quite disturbing, but i was only 11 when i played it; i had to ask a guy to buy it for me. xD That thing with the dog through the window is just a classic. Silent hill 2 was pretty bad back then. That asylum levels in thief 3 (was it 3?) been quite a thing too. Anyone remembers system shock? That much for the classics. Pokemon black would be quite disturbing IF it exists.

Dead Space was very disturbing after a while. The fleshy mutations were bad when they moved and worse when they covered the floor in body parts. And the hard metal surfaces didn't help.

FEAR too, especially the main plot. Icky.

Realms of the Haunting was consistently unsettling. The ending sealed it.

Silent Hill series, of course. Parasite Eve, Galerians.

Grandia 2, believe it or not. The presentation is cutesy but the themes are disturbing.

Project Eden, a little.

I never found Planescape: Torment disturbing. It was too intellectual and matter-of-fact to disturb. Surreal is a better description. But player decisions can lead to some very disturbing outcomes.

Top one for me is Soldier of Fortune. Your enemies scream and flail for a while when their limbs are shot off. I have high tolerance for realism in games, but this one was over my moral threshold.