The condemned series, with the brightness slightly under what they recommend so you are required to have your flashlight is the only game that has managed to freak me out. If you had any issues with stalker/fear than you won't even be able to play condemned. FEAR/stalker is childish compared to it.
Get a good 5.1 system, crank it, play the game at night, and turn the lights completely off.
However i'm not sure how good these games are on the PC.
Vampire the Masquerade: Bloodlines is also a good game, its rather old though. Get the player made patches if you do get this game.
Honestly, I find games with deep water/underwater creatures scary... I'm not sure why but I have a very hard time swimming knowing theres *something* down there. I have no issues swimming IRL though... but I don't think I could swim in the ocean.