Every one of the Parasites deserves what they got, but killing Doctor X somehow feels the most rewarding. Probably because s/he gets the most build-up.
Killing the Second and Third Parasites is awesome in a particularly Troperiffic way. Turning all the B-Movie horror they've inflicted on Susan back against them is incredibly satisfying.
Getting the ending where Mitzi lives. It's just so full of feelings, there is no words.
Susan overcoming her depression and self-loathing by defying their anthropomorphic representation, the Queen of Maggots, and refusing to blow out a candle. Made especially powerful by the voice actress's soft but conviction-filled delivery on: