I think the most scariest game I ever played was the system shock remake. at least back in the day it was super creepy..and eerie...friggin mutants >_>
@Lufffi: BioShock... I had nightmares... serriously, that game scares the crap outta me. The only warning you get is like 2 seconds of music... and ofcourse theres the insane splicers that talk to themselves... creepy. Plus, you never know where an enemy is, unless its a Big Daddy/Rosie. Even the opening sequence was kinda freaky... the elevator stops, lights are flickering... and the jacked up splicer shows up! he freakin trys to break through the elevator just to kill you! I kept on thinking I was gonna die right when I stepped out...
I don't know if this counts... since it's not a game... but the most emotionaly disturbing thing I have ever seen is Silent Hill. The freakin Pyramid Head guy grabs that girl, rips her clothes off (no obscene material there, her back was to the camera) and then goes and rips her skin off!!! The demon babies freaked me out even more...