When I was younger, Friday the 13th on the NES used to freak me out... 8-bit graphics and sound can be unnerving when they're trying to be scary and you're playing the game all alone with no one around you. Really, it was the 3rd person house roaming parts when you got to a house that Jason was in... that feeling that "Son of a *****, he's right THERE... to my left or right."
A little later on, Splatterhouse 3 freaked me out a good bit, mostly from the digitized cut scenes of the real actors. Same deal, 16-bit graphics and sound are creepy as hell when they're trying to be scary... so it worked. Also the level 3 boss when you go to rescue your son... look it up. *shudders*
The stupidest "makes you jump out of your seat" moment I had with a game was in the Star Trek: The Next Generation game on Sega Genesis/SNES. The Red Alert would set itself off every time I was settling in to do something... didn't help it tended to be louder than any other sound effect in the game and I'd usually be playing when the house was totally silent. Would startle the shit outta me.
I can't say if any more modern games have scared me that much... it's usually all cheap sudden reaction scares which just get annoying. I love horror movies too much to be scared anymore, it certainly won't bother me in a game. When it came to something like Resident Evil, I was too aggravated with the controls to be freaked out by anything.