Here's an updated list of mine with a few more companies and I decided to add one more character to each company but I think I'm going overboard.
Nintendo:
Peach, Fox, Lucario, Roy, Zelda, Little Mac, Captain Falcon
Sega:
Silver, Bayonetta, Shinobi, Ryo Hazuki, Ulala, Altered Beast, Akira
Capcom:
Mega Man, Jon Talbain, Leo, Rose, Chibiterasu, Strider Hiryu, Chris Redfield
Namco Bandai:
Klonoa, Red Savarin, King, Nightmare, Ivy, Blackwargreymon, Waffle Ryebread
Square-Enix:
Vincent Valentine, Sorceress Edea, Kimahri Ronso, Lynx, Melissa Pearce/Eve, Marluxia, Culex
Konami:
Solid Snake, Bomberman, Simon Belmont, Pyramid Head, Cornell, Goemon, Yugo
Ubisoft:
Rayman, Ezio Auditore da Firenze, The Prince, Aiden Pearce, Raving Rabbid, Jade, Sam Fisher
Rare:
Banjo & Kazooie, Conker, Joanna Dark, Fulgore, Rash, Juno, Cinder
Sony:
Kratos, Nathan Drake, Ratchet and Clank, Sly Cooper, Jak & Daxter, Cole Macgrath, Journey
Microsoft:
Master Chief, Marcus Fenix, Blinx, Steve, Brutus, Gideon Wyeth, Bullet Witch
Indies:
Shovel Knight, Shantae, Meat Boy, Dust, Quote, Commander Video, Foxy
Electronic Arts:
Commander Shepard, Garrus Vakarian, Alcatraz, Faith Connors, Dante, Isaac Clarke, Army of Two (similar to the Ice Climbers)
Activision:
Exo, Colton White, Katia, Alex Mercer, Angry Birds, Spyro the Dragon, Crash Bandicoot
THQ:
War, Death, de Blob, Sphinx, Nevin, Tak, Drawn to Life