The scariest game Ive ever played is SILENT HILL 2 on the PS2.
Alone in the house, lights off and with headphones on. :shudder:
This game is scarier than any film Ive watched. (especially the old prison section)
Also in a strange way Tomb raider used to give me the creeps. Walking through dark areas with only a flare was creepy.
On the Amiga it would have to be SPACE HULK. VERY scary for its time.