Clockto- Dammit Stranger 517!
Yeah, Clocktower is brilliant. Scary as all.
It's old. Ancient, actually. But Zork Nemesis, only for PC, is rather creepy in its own right. It wasn't that way intentionally. It was, what, the whole 'dragging a corpse in an attempt to reanimate the head so you could learn some clue' thing...
In a similar note, 7th Guest and 11th Hour are old, also only for PC, and are about hanging around in a haunted house point&clicking puzzles away in creepy scenarios to thwart a talking skull with eyes.