My favorite of all time is Marvel vs Capcom 2 (arcade or Dreamcast) just because the roster is ridiculous and the move sets are insane. Plus it has Venom, Akuma, AND Blackheart
I felt the Dreamcast port was closer to the arcade than the PS2 version.
Other great titles:
KOF '98 (Neo Geo)
Garou: Mark of the Wolves (Neo Geo - arguably the most balanced and intricate skill curve of any fighting game of all time)
Soul Caliber II (favorite 3D fighter)
Guilty Gear 2 (Dizzy <3)
BlazBlue: Calamity Trigger
notable mentions go to SSF4, SF3: 3rd Strike, Super Smash Brothers Melee, and Samurai Showdown V(arcade, never played the home port)