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That's a pretty good list right there. I can't think of anything that shouldn't be there.Mario Universe: Bowser (playable), Bowser Jr. (playable?), Koopalings
Zelda Universe: Ganondorf (playable?), Vaati, Fyrus/Stallord/Armagohma/etc
Kirby Universe: King Dedede (playable), Meta Knight (playable), Dark Matter
Pokemon Universe: Mewtwo (playable?), Shadow Lugia, Darkrai
Starfox Universe: Andross (head), Wolf (playable?)
Metroid Universe: Ridley (playable?), Dark Samus (playable?), Mother Brain, Omega Pirate
DK Universe: King K. Rool (playable?), Army Dillo/Mad Jack/etc
Yoshi Universe: Kamek, Baby Bowser, Raphael Raven
Ice Climber Universe: At best, a crossover fight. There were no bosses in Ice Climber anyway.
Kid Icarus Universe: Medusa
Wario Universe: Rudy the Clown, Capitan Syrup, something from Warioware (never played)
Fire Emblem: The Black Knight (playable?), any other FE boss (havent played FE)
MGS Universe: Metal Gear REX/RAY/something, Liquid Snake, Psycho Mantis, etc
Mother Universe: Claus (playable?), Yokuba, Porky
Sonic Universe: Chaos 0/1/2/3/4/5/6/Perfect, Biolizard, Iblis, Metal Sonic, Dr. Robotnik
Pikmin Universe: Orange Bulborb, Emperor Bulborb, a Dweevil boss
F-Zero Universe: Black Shadow (playable?)
Just my two cents.