The Gargant in HL was also pretty scary.
Scariest is when they completely take you by surprise though, and I find that because you experience a few moments of complete lack of thought, it really doesn''t matter what came at you.
I remember playing some Aliens-like game, where I was running around, and then out of no-where, about fifteen of the medium-level aliens jumped at me from the ceiling (side-scroller), I wasn''t really in danger, but I was jumpy as all hell for a good half hour.

Are you in support of the ban of Dihydrogen Monoxide? You should be!