
I have a soft spot for the Half Life crab/spider thing sub boss before you got to the disapointing end boss. It was the size of the thing and sound it made when it began a charge at you. Also was pretty unusual compared to everything that had gone on before.

Mgs4 snake-liquid cqc fight at the end, with all the flash backs and backround songs. Pure epic
Shub-Niggurath!
Sephiroth from FF7 (technically a console game, but I had it on PC as a kid).
He made me cry when he killed Aeris (I think I was 10-11 at the time). The sad thing was, I kept dying on the boss directly after that cutscene, so I had to keep replaying it.

. It took us about 2 hours... man was it intense. Best boss ever.Mgs4 snake-liquid cqc fight at the end, with all the flash backs and backround songs. Pure epic