Helplessness is probably the largest element in a true horror game. Take Amnesia for instance. You have no weapons, a sanity meter, and enemies that could mutilate you at any second.
Creepy atmosphere isn't far off. Dead Space really capitalizes on that, with dead bodies everywhere and blood lining the walls. Plus, the monsters are still wearing clothing.
BOO moments can be hard to expect, but then there's also those "WHAT THE HECK IS THAT!!" moments. The BOO moments are those jump-out-of-your-chair things. "What the heck is that!" moments are when a monster walks slowly across a hallway, adding greatly to the suspense. Plus, you don't know it it's going to see you or not.