Insert "omg pussies that games wasnt scary at all" or "I never get scared by games anymore. Not by anything really." here. That's what's going to happen in this thread, guaranteed.
Metroid Prime 3 made me jump out of my skin on the G.F.S. Valhalla, where you open a door and suddenly a corpse is standing in front of you disintegrating.
But scariest game? FUCKING HELL, download Afraid of Monsters. Not only is it a classic hospital setting, but monsters spawn everywhere and at random depending on how you're doing, like left for dead. Also, it's the HL1 engine which strangely makes it more scary due to the bad graphics.