Updated List:
Mario Series:
Mario
Luigi
Peach
Daisy
Toad
Bowser
Bowser Jr.
Boo
Geno
Paper Mario
Dr.Mario
Cheep Cheep
Waluigi
Birdo
Dry Bones
Monty Mole
King Bomb-omb
Koopa Troopa
Wart
Shy Guy
Blooper
Fawful
Legend of Zelda Series:
Link
Young Link
Wolf Link
WW Link
Goron
Zelda/Sheik transformation
Zelda/Tetra transformation
Tetra by herself
Ganondorf
Tingle
Midna
Vaati
Cucoo
Skull Kid
Ralph
Veran
Onox
Octorock
Twinrova
F-Zero Series:
Captain Falcon
Black Shadow
Pico
Rick Wheeler
PJ
Mighty Gazelle
Spade
Pokemon Series:
Pikachu
Pokemon Trainer with Squirtle, Ivysaur, and Charizard
Jigglypuff
Lucario
Mewtwo
Geodude
Pichu
Mew
Deoxys
Darkrai
Spiritomb
Gallade
Scyther
Typhlosion
Magmortar
Arceus
Pokemon Master- with Duskull, Lairon, and Dragonite
Haunter
Fire Emblem Series:
Marth
Ike
Hector
Micaiah
Roy
Sigurd
Eliwood
Black Night
Leaf
Ephraim and Eirika
Earthbound Series:
Ness
Lucas
Claus
Jeff
Pokey
Ninten/Loid/Ana as one character
Poo
Starman Junior
Kumatora
Flint
Kirby Series:
Kirby
Metaknight
King Dedede
Waddle Doo
Rick
Animal Trio- Rick, Kine, and Coo
DK Series:
Donkey Kong
Diddy Kong
Dixie Kong
King K. Rool
Funky Kong
Lanky Kong
Chunky Kong
Tiny Kong
Metroid Series:
Samus/ Zero Suit transformation
Ridley
Dark Samus
Kraid
Space Pirate
Rundus
Sylux
Noxus
Ingmaster
Star Fox Series:
Fox
Falco
Krystal
Wolf
Peppy
Slippy
Wario Series:
Wario
Jimmy
9-Volt
Ashley
Kat and Ana
Mona
Captain Syrup
Yoshi Series:
Yoshi
Kamek
Ice Climbers Series:
Ice Climbers- Popa and Nana
Game and Watch Series:
Mr. Game and Watch
Kid Icarus Series:
Pit
Balloon Fighter Series:
Balloon Fighter
Mach Rider Series:
Mach Rider
Pong Series:
Pong Paddles
Pac-Man Series:
Pac-Man
Chrono Trigger Series:
Crono
Magus
Frog
Robo
Marle
Golden Sun Series:
Issac
Ivan
Felix
Custom Robo Series:
Ray 01
Rahu
Pikmin Series
Captain Olimar
Animal Crossing Series:
Animal Crosser
K.K. Slider
Sonic Series:
Sonic
Tails
Knuckle
Espio
Metal Gear Series:
Snake
Megaman Series:
Megaman
Megaman X with Zero incorporated
Protoman
Bass
Zero
Bomberman Series:
Bomberman
Rayman Series:
Rayman
Viewtful Joe Series:
Viewtful Joe
Trauma Center Series:
Dr. Stiles
Ace Attorney Series
Phoenix Wright
Ninja Gaiden Series:
Ryu Hayabusa
Tales Of Symphonia Series:
Lloyd
Kingdom Hearts Series:
Sora
Riku
Ratchet Series:
Ratchet and Clank
Advance Wars Series:
Andy and Will
Profesor Layton and the Curious Village Series:
Proffesor Layton
Mole Mania Series:
Muddy Mole
Adventure of Lolo Series:
Lolo and Lala
Star Tropics Series:
Mike Jones
Mischeif Makers Series:
Marina Liteyear
Casttelvania Series:
Simon Belmont
Cluclu Land Series:
Bubbles
Tomato Adventure Series:
Demiru
Joy Mecha Fight Series:
Sukapon
Panel De Pon Series:
Lip
Osu! Tatakae! Ouendan Series:
Ippongi Ryuta
Nazo no Murasame-jō Series:
Takamaru
Pro Wrestling Series:
The Amazon
Hulk Hogan
Super Smash Series:
Master Hand
Fighting Wire Frames
Polygon Team
Nintendo Hardware Series:
Pictochat Stick Figure