I haven't played too many horror games, I'll have to give you that. Some of the games I've played and like did have really fucked up parts - Max Payne, for example, when you're on drugs... Of course, when I played it I was like 10 so the effect might have been different but running through snow falling down over nothingness, forcing to crawl over unreal tubes suspended over that nothingness and hearing endless psychotic laughing of some deranged man talking about a fictional comic book character from the game (it was something about killing people with baseball bat) while someone is crying and being beaten on in the background. That was pretty freaky.
Other then that, there's always the cheap startling option... And of course, the whole "distant stalker" thing can become really creepy in the right environment - I remember playing one of the early AvP games, probably the first one, the beginning of the human campaign. At one point you had to restore power to an elevator and, well, use it to lift yourself against a practically flat cliff into further passage. It's very dark and empty... But as you almost reach the "top floor", you notice Aliens climbing this absolutely vertical cliff. They're too far to actually hit, you can only see them from afar - there are only like 2 or 3 of them. They keep their distance, slowly climbing behind you... And then you're finally further into some kind of dark corridor, and you can barely discern various ventilation shafts around you, and you KNOW that aliens will come through them sooner or later and still hear those 2 pursuit you from outside.
Okay, I still haven't pitched an idea... How about this: It'd start out as a fairly usual supernatural horror game. There is a handful of survivors, and some really creepy, fucked up monsters that seem really threatening. But at some point into the game, you realize that the monsters aren't what you should be really afraid of, it's your own fellow survivors that are the true horror. And you probably end up fleeing them or murdering them in a graphic display of gore, your victims both being innocent and at the same time menacing - and the sense of danger has to be VERY real, and the same for the acts of violence against them.
Basically, yeah, huge twist - you end up hunting down your fellow survivors and end the game killing the last one in some small exposed room or building with see-through walls/ huge windows. There's a lightning storm and whenever there's enough light you can see true lovecraftian horrors pressed against the windows. Then you kill the last survivors and wonder... Am I still the survivor? Or am I one of the monsters? Of course, for more freedom there could be more paths to the game - you could try to avoid the other survivors even after seeing then obvious evidence of them trying to kill you. But that would make you even more hunted, both by the strange monsters and the survivors. Or you can back away from the deed only to be backstabbed by the other survivor, possibly then continuing playing from his or her point of view.
In short, the premises would be: It's dark, strange and "shitting bricks" level of fucked up and unreal. The people seem real and the writing should make real attempts to make you care about other "survivors". But in the end the real monster is the player, and all that is done from a perspective of a helpless game, not some kind of cold blooded hunter one can consider oneself in certain FPS or semi-horror games.
How about that?