Scariest thing I've ever experienced was in Thief 2, when I first encountered the tree monsters. Normally, they just sit there, looking like a perfectly harmless tree, until you sneak by them, and then they make the most godawful sound and start chasing you. And when one starts chasing you, the others wake up too, and you quickly get twenty of the sods after you.

I've also never been able to finish either of the two System Shock games, since they utterly creep me out.