F.E.A.R and
Slient Hill (I only played the first one) are good examples of how to do that.
Silent Hill was scary and disturbing because of:
Audio - You hear the PC's breath, heart beat, echoes, and everything else tends to be fairly quiet until your getting attacked by something
Imagery - The world around you gradually got darker as the game progressed, lighting was very important, there was plenty of blood, sharp objects laying around, and butchered bodies. This stuff was every where. The PC would tremble constantly. You had to watch bad things happen that you could not stop.
Gameplay - You were a clumbsy, shaking, unauthentic, ordinary joe clutching a little crow bar, trying to save his daughter, in a world full of athletic demonic creatures that what to kill you. Even worse, everything you did only made that world more harsh.
F.E.A.R was scary and disturbing because of:
Imagery - The PC would have random "delusions" where your vision becomes blurry and figures in the dark try to attack you or they do bad things that you want to stop. Things would randomly fall from the ceiling when you walk up on them, cinematic events were triggered often and in places you may not expect. You could never stop the bad things from happening, you had to sit through them.
Audio - You hear whispers in the dark and are constantly taunted by voices that you cannot reach.
Gameplay - During "halucinations" your character still had the ability to move but and shoot but you were much slower and shooting didn't always have an effect. Also, it wasn't clear whether the things you saw existed in the real world or not. Then the episodes would end abruptly and leave you where you were before you started making it seem as though you must have been hallucinating.
I think the key to making a game "disturbing" is the ways in which you take control out of the player's hand but still include them in the action. Silent Hill did this by making your character physically weak and shakey (this did annoy some, but I appreciated the change from the Resident Evil way), and F.E.A.R did this with well timed scenes of hallucinations that were beyond the PC's control, and both subjected the player to cinematic scenes of things they would want to stop but could not.
I also think the second biggest element is timing. By timing event's to occur when they are least expected, or at least when they are least desirable, you keep the player on their toes. After that there is pacing; by allowing the player to slow down and think things are ok you prepare them to be surprised again when things are not ok. Of course that is partly related to timing, but it is important to slow things down or the effect of surprise wears off and turns into fatigue and grinding.
So if you effectively leverage the players freedom to engage in the action against their handicaps, employ good timing, and keep up a well varied pace you can create a "scary" atmosphere. You should also use sound effects (I believe this is the more important factor) and imagery to heighten the suspension of disbelief.