A good scary game relies very heavily in the use of atmosphere. Sound, lighting (total absence of light is not lighting, it's "darkening"), and level design play a huge role in that. Music too, if used very sparingly and at key points. The enemies themselves don't need to be numerous nor aesthetically repulsive. But they need to be able to keep you on edge. AvP and AvP2 are probably the only games that have been able to keep me on edge every single second on the first playthrough.
Doom 3 does none of that. It just has ugly monsties and overuse (the understatement of the year) of dark areas. It had pretty graphics too, I guess.