Mine is Silent Hill 3. Its subject matter revolves around the fears of a teenage girl, like death of a parent, puberty, unwanted pregnancy (with a demon fetus, no less), mirrors (THAT ROOM shivers), and stalkers. The atmosphere is so oppressive and I cant play the game without having something else playing in the background, its that horrifying. I managed to finish Silent Hill 2 last year, which was like conquering my own fears. One day, I'll finish SH3. One day.
SOMA may be my second favourite game of all time. I highly recommend it to everyone. Even if you don't normally do scary games (like me, I'm a total wuss), there is a safety mode where the monsters cannot kill you. This makes it tolerable enough for even people like me to experience the game, and its amazing atmosphere and story.