SNES:
Art of Fighting 1 & 2
Battle Master
Clay Fighter: Tournament Edition and Clay Fighter 2: Judgment Clay (Unlock All Bosses Hack)
Dead Dance (also known as Tuff E Nuff; the original Japanese version has character quotes and endings)
Fatal Fury Special
Fighter's History (Unlock Clown and Karnov Hack) and Mizoguchi's Moment of Crisis
Killer Instinct
The Gundam Fighting Games (Mobile Fighter G Gundam and Gundam Wing: Endless Duel)
Makeruna! Makendou 2
Mighty Morphin Power Rangers: The Fighting Edition
Mortal Kombat II and Ultimate Mortal Kombat 3 (MSU-1 Mod)
Power Instinct
The Ranma 1/2 games (Hard Battle and Chougi Ranbu Hen (Improvement Hack))
Sailor Moon Fighter S
Samurai Shodown
Saturday Night Slam Masters (technically it's more of a wrestling game)
The Street Fighter games (Turbo, Super, and Alpha 2 (MSU-1 mod))
Teenage Mutant Ninja Turtles: Tournament Fighters
World Heroes 1 & 2
The YuYu Hakusho games (Kakutou no Shou and Final)
Genesis:
Eternal Champions (Easy Difficulty Hack)
Fatal Fury 1 & 2 (Unlock All Bosses and Color Improvement Hack)
Fighting Masters
King of the Monsters 2 (this version is a fighting game rather than a beat-em up)
The Mortal Kombat games (MK: Arcade Edition, MK II Arcade Edition 32X, and Ultimate MK Trilogy (this one requires a special modified version of the GENS emulator (GENS Plus Mod) to play with))
Power Instinct
Samurai Shodown
Saturday Night Slam Masters (this version allows you to play as Jumbo and Scorpion in 1 Player Mode)
Sega Master System Brawl (homebrew game)
The Street Fighter games (Special Champion Edition Remastered and Super)
Street Smart
Teenage Mutant Ninja Turtles: Tournament Fighters
The Virtua Fighter games (Virtua Fighter 32X and Virtua Fighter 2 Genesis)
YuYu Hakusho: Makyo Toitsusen