I'm one-note on this, but my favorite RPG of the '90s was the one I probably played most:
Street Fighter: The Storytelling Game.
I noticed that, like a lot of others, many of the games I was considering are technically from the later '80s, but here are three more that fit in there fairly high:
Heavy Gear
Vampire: The Masquerade
Castle Falkenstein
Unfortunately, I usually get stuck RPing in some kind of D&D-ish fantasy thing these days. I am playing in a semi-regular DC Heroes 3rd ed. game as well, though, so I won't complain too much.