Just talking about the one-on-one stuff here, not the brawlers.
List your top ten/five/two/one/whatever. Here are my fab five:
#5 Godzilla
Excellent presentation, and controls that are much smoother than they're typically given credit for.
#4 Kabuki Ittouryoudan
An SF2 clone, to be sure, but it feels great. And, being a Kabuki Den fan, I love the cast of characters.
#3 Street Fighter 2' CE
f*cking awesome port, though I can't help but yearn for the speed and audio of SNES Turbo.
#2 Art of Fighting
Technically, this should be a couple spots lower, but it's kind of a personal favorite, as I really dig the gameplay. Go figure.
#1 Asuka 120%
Gives me everything I could ask for in a fighter: fast gameplay, smooth controls, great music, accessible action, fun characters and attack moves, good multiplayer, and a few cute girls.
I've played a bunch of others (Advanced VG, Fatal Fury Special and 2, Ranma 3, Fighting Street...), but those five are head and shoulders above them.
Two that I haven't tried yet are Flash Hiders and World Heroes 2. Some reshuffling may be in other after I get my hands on those.