The whispering voices always creeped the heck out of me. Also, there was that scene where you encounter the first Lost Soul, where the woman's head just comes off and starts floating toward you. That freaked the hell out of me. One thing I never found scary? Any one of the countless jump scares. I think jump scares are silly, stupid, and pointless. The scariest movies are always the ones that scare you by building atmosphere, not having monsters jump out of closets. I mean, in my opinion, The Thing is the scariest movie I've ever seen, and while it does use the occasional jump scare, it earns those moments. The primary cause of fear and dread in that movie isn't the jump scares themselves, it's the paranoia the movie creates via its atmosphere.
Basically, the scariness of any form of media should be based on this - are you afraid even when the monster isn't onscreen, when nothing significant is happening? 99% of the time, I didn't feel that way with Doom 3. It had those moments, like the whispering voice telling you to follow it, and I was seriously creeped out then, but those were few and far between. Most of the time, I'm just running around like, "Okay, what do I get to shoot next?" Actually, that's what made the whispering so creepy - monsters I can handle, a shotgun to the face is a useful strategy. You can't shoot a whispering voice, though, and you have no idea if your weapons even matter when dealing with things like that. The unknown - that's scary. What's the point in having monsters jump out at me when I already know I can blow 'em away with my boomstick?
And don't get me wrong, an action game can be scary - take F.E.A.R., for example. Yeah sure, in that game, enemies go down with a shotgun to the face, too, but that wasn't what was scary. What was scary was the creepy ghost girl who could do whatever she wanted to you and you couldn't fight back. Plus, half the time you had no idea if what you were seeing was reality. You could mow down an army of enemy soldiers, but that wasn't the point. The game made you paranoid because you didn't know what the main antagonist was capable of. Friggin' Alma could explode people, make you hallucinate, teleport you, possess people, etc., so you spend the whole game wondering if at any moment you're going to become a bloody pile of goop pasted on the walls, and it's not like any of your guns meant anything against that.