In terms of overall scaryness Silent Hill 1.
In terms of shock factor(things that make you jump) Resident Evil 2.
Those are the game at the top of my scary list from when I was a kid playing them the first time.
Have to also add Alien Trilogy if you played it now you'd laugh but playing it as a kid that game was disturbing especially when you got killed and it showed an FMV of the way you died.
The most disturbing moment in a game for me though was in Max Payne 1 when he'd just been spiked with valkrie and started tripping... the main reason it disturbed me though was because I too was tripping and was just like :O
