The VG Resource

(BTW gonna be lots of stuff here that's already been brought up)

Also, going with the 5 companies and 8 characters option, to afford some villain representation.

Nintendo
-Mario
-Link
-Samus
-Pikachu
-Kirby
-Fox
-Bowser
-Ganondorf
Capcom
-Megaman
-Ryu
-Dante
-Arthur
-Zero
-Dr. Wily (in a modified form of his MM Soccer suit)
-M. Bison
SNK (yeah, sorry for the dominance of KoF here)
-Terry Bogard
-Kyo Kusanagi
-Haohmaru
-Marco Rossi
-Athena
-Ryo Sakazaki
-Rugal Bernstein
-Amakusa
Konami
-Simon Belmont (with various bits and bobs cannibalized from other Belmonts)
-Solid Snake
-Alucard
-Bombeyman
-Goemon
-Pentaro (hi, requisite out-of-left-field callback character)
-Dracula
-Revolver Ocelot
SEGA
-Sonic
-Akira Yuki
-NiGHTS
-Alex Kidd
-Temjin (Virtual On)
-Toejam and Earl (dual character a la Ice Climbers)
-Shadow the Hedgehog
-Dr. Robotnik

It's hard to decide so I've done it both ways:

Sega
Sonic the Hedgehog (Classic, Modern, Boom, Super Sonic recolour)
Jacky Brent [from Virtua Fighter] (Current, Model 1 [VF1], Model 2 [VF2], Model 3 [VF3])
Joe Musashi (Current, Shinobi, Revenge of Shinobi/Shinobi 3, Hotsuma)
Blaze Fielding [from Streets of Rage]

Namco
Klonoa
Dr. Don and Dr. Dan [from Point Blank]
Heihachi [from Tekken]
Jack Slate [from Dead to Rights] (Max Payne exipy)

Capcom
Mega Man (Original, X, Legends, Battle Network)
Mike Haggar [from Final Fight] (Original, Final Fight 3, Mayor outfit, Slam Masters style)
Nathan Spencer [from Bionic Commando] (Original, 2009, Rearmed, Super Joe from the arcade version)
M. Bison [from various Street Fighter games] (Original, Alpha 2, Movie, Shin Bison)

Konami
Solid Snake [from Metal Gear Solid]
Richter Belmont [from Castlevania: Rondo of Blood] (Simon Belmont recolour, Juste Belmont recolour, Trevor Belmont recolour, Leon Belmont recolour)
Sparkster [from Rocket Knight Adventures] (Original, Sparkster, Rocket Knight, Axel recolour)
Gillian Seed [from Snatcher]

Ubisoft
Rayman (Classic, Origins/Legends, Prototype)
Aveline [from Assassin's Creed III: Liberation]
Sam Fisher [from Splinter Cell] (Classic, Blacklist, Double Agent, Conviction)
Rex Power Colt [from Far Cry 3: Blood Dragon] (Default, Spandex, Godfrey Ho styled Ninja, other 80s style look here)

Warner Bros.
Batman [well he appeared in various games...] (Current look, TAS, Adam West, Year One)
Scorpion [from Mortal Kombat] (MK9 look, Classic as in the digitized fighter look, Injustice look, Sub-Zero recolour)

WayForward (not much choice...)
Shantae
Patricia Wagon [from Mighty Switch Force] (Police officer, Firewoman, bikini, Luna from Mighty Milky Way)

Console exclusives:

Nintendo
Mario (Fire Mario, Luigi recolour, Wario recolour, Waluigi recolour)
Donkey Kong
Fox McCloud [from Star Fox] (Original, Current, James McCloud, Falco)
Captain Falcon [from F-Zero]

Sony
Nathan Drake [from Uncharted]
Ratchet & Clank
Sly Cooper (Classic, Thieves in Time, Movie)
Gabe Logan [from Syphon Filter] (Sony forgot about him on PlayStation All-Stars)

Would have put Crash for the Sony one except that they don't own him so had to resort to another PS1 character.

Microsoft
Master Chief [from Halo]
Banjo-Kazooie (Original, Nuts and Bolts)
Joanna Dark [from Perfect Dark] (Original, Zero, Tuxedo [to reference GoldenEye], Kameo style [to reference the other 360 early title by Rare])
Blinx [from Blinx: The Time Sweeper] (presumably they have the rights to this game?)

Had ideas for a Rockstar roster (including Phil Collins) and a joke EA one however it is over the 10 company limit. Also with the 5 company/8 character alternative decided to choose a multiplatform angle (since having the 3 console companies and PC would limit the other companies):

Sega (too hard to decide...)
Sonic the Hedgehog
Dr. Robotnik/Eggman
Jacky Brent [from Virtua Fighter]
Joe Musashi [from Shinobi]
Blaze Fielding [from Streets of Rage]
Robo and Mobo [from Bonanza Bros.]
Beat [from Jet Set Radioooooooooooooo]
Vyse [from Skies of Arcadia]

Capcom (not easy)
Mega Man
Dr. Wily
Mike Haggar [from Final Fight]
Nathan Spencer [from Bionic Commando]
M. Bison [from various Street Fighter games]
Frank West [from Dead Rising]
Lord Raptor [from Darkstalkers]
Jill Valentine [from Resident Evil]

Namco
Klonoa
Dr. Don and Dr. Dan [from Point Blank]
Heihachi [from Tekken]
Jack Slate [from Dead to Rights] (Max Payne exipy)
Bravoman
Reiko Nagase [from Ridge Racer Type 4/64]
Nightmare [from Soul Calibur]
Dweeb [from The Outfoxies]

Konami
Solid Snake [from Metal Gear Solid]
Richter Belmont [from Castlevania: Rondo of Blood]
Sparkster [from Rocket Knight Adventures]
Gillian Seed [from Snatcher]
Cormano [from Sunset Riders]
Male and female characters [from Bishi Bashi Special] (I don't think that they have names, blue hair man and blonde woman)
Goemon
Dingo Egret/Jehuty [from Zone of the Enders: The 2nd Runner]

Square-Enix (Europe and Taito mostly)
Agent 47 [from Hitman]
Lara Croft [from Tomb Raider]
Wei Shen [from Sleeping Dogs]
Adam Jensen [from Deus Ex: Human Revolution]
Bub and Bob [from Bubble Bobble/Puzzle Bobble]
Sonic Blast Man
Black Lotus [from Bushido Blade]
A Final Fantasy character here [not into RPGs sadly to choose a character]

I'm lazy and tired and hungry. Goodbye.

Maaaaan, it's so hard to choose.