Maaaaan, it's so hard to choose.
Nintendo
Mario
Kirby
Donkey Kong
Link
Pit
Samus Aran
Olimar
Sony Computer Entertainment
Sly Cooper
Jak and Daxter*
Ratchet and Clank*
Crash Bandicoot (not sure if this should count)
Spyro the Dragon (or this)
Spike [Ape Escape]
Parappa the Rapper
SEGA
Sonic the Hedgehog
AiAi [Super Monkey Ball]
Billy Hatcher
Alex Kidd
NiGHTS
Ristar
ToeJam and Earl*
Gunstar Red [Gunstar Heroes]
Konami/Hudson Soft
Bomberman
Simon Belmont [Castlevania]
Solid Snake [Metal Gear]
Bonk
Master Higgins [Adventure Island]
Goemon [Mystical Ninja]
Capcom
Mega Man
Mega Man X
Ryu [Street Fighter]
Phoenix Wright [Ace Attorney]
Amaterasu [Okami]
Arthur [Ghosts & Goblins]
Dante [Devil May Cry]
* - Dual character, like the Ice Climbers
Nintendo
Mr. Game & Watch
Stanley the Bugman [Donkey Kong 3]
Mallo [Pushmo]
Dillon
Lip [Panel de Pon]
Hawk [Pilotwings]
Muddy Mole [Mole Mania]
Namco-Bandai
Pac-Man
Ms. Pac-Man
Klonoa
Mr. Driller
Bravoman
Mappy
Wayforward Technologies
Shantae
Patricia Wagon [Mighty Switch Force]
Alta [Mighty Flip Champs]
Luna [Mighty Milky Way]
Konami/Hudson Soft
Penta [Penguin Adventure]
Milon [Milon's Secret Castle]
Sir Cucumber [Princess Tomato in the Salad Kingdom]
Twinbee
Vic Viper [Gradius] (sure, why not?)
Capcom
Mega Man Volnutt [Mega Man Legends]
Viewtiful Joe
Sissel [Ghost Trick]
Zack and Wiki*