If you manage to get a playthrough where Scissorman shows up quite a bit then it's one of the freakiest games you'll ever play. The music, the atmosphere, the lack of ability in fighting back, and the creative and randomized entrances for the main threat makes this one of the scariest games ever created.
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Echo Nights - The one where you're in space was a good one (never played the first one on the boat)
Condemned - The first game was actaully really scary O.O
Fatal Frames 1 - This game.........omg this game.
Clock Tower 3 - hmm this game might have been more heart pounding thrilling than scary *shrug*
They Hunger - seriously, I'm not Kidding.
out of this short list I think I would go with Fatal Frames 1. It's the only game out of all of them that actually physically made me stop playing. The game would pressure me out so much I would ether trade off with my sister or just stop playing until i calmed down lol.
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