Koopa Troopa (Super Mario Bros. - 1985)
Hammer Bros. (Super Mario Bros. - 1985)
Toad (Super Mario Bros. 2 - 1988 )
Petey Piranha (Super Mario Sunshine - 2002)
Geno (Super Mario RPG: Legend of the Seven Stars - 1996)
Cel-Shaded Link (The Legend of Zelda: The Wind Waker - 2002)
Tetra (The Legend of Zelda: The Wind Waker - 2002)
Link's Uncle (The Legend of Zelda: A Link to the Past - 1991)
Ganon/Ganondorf (The Legend of Zelda/The Legend of Zelda: Ocarina of Time - 1986/1998 )
Bow Wow the Chain Chomp (The Legend of Zelda: Link's Awakening DX - 1998 )
Ridley (Metroid - 1986)
Peppy Hare (Star Fox - 1993)
Slippy Toad (Star Fox - 1993)
Krystal (Star Fox Adventures - 2002)
Wolf O'Donnell (Star Fox 64 - 1997)
Diddy Kong (solo) (Donkey Kong Country - 1994)
Diddy Kong & Dixie Kong (Donkey Kong Country/Donkey Kong Country 2: Diddy Kong's Quest - 1994/1995)
King K. Rool (Donkey Kong Country - 1994)
Ninten (Mother - 1989)
Jeff (Mother 2 [EarthBound in the U.S.] - 1994 [1995])
Claus (Mother 3 - 2006)
Lucas (Mother 3 - 2006)
King Dedede (Kirby's Dreamland - 1992)
Lololo & Lalala (Kirby's Dreamland - 1992)
Marx (Kirby Super Star - 1996)
Oguma (Fire Emblem: Ankoku Ryuu to Hikari no Tsurugi - 1990)
Nabarl (Fire Emblem: Ankoku Ryuu to Hikari no Tsurugi - 1990)
Sigurd (Fire Emblem: Seisen no Keifu - 1996)
Ike (Fire Emblem: Path of Radiance - 2005)
Mia (Fire Emblem: Path of Radiance - 2005)
The Black Knight (Fire Emblem: Path of Radiance - 2005)
Black Shadow (F-Zero X - 1998 )
Eggplant Wizard (Kid Icarus - 1986)
Isaac (Golden Sun - 2001)
Felix (Golden Sun: The Lost Age - 2002)
Little Mac (Punch-Out!! Featuring Mr. Dream - 1990)
Dragon Chan (Super Punch-Out!! - 1994)
Banker (Mario Paint - 1992)
Ray 01 (Custom Robo - 2004)
Captain Olimar (Pikmin - 2001)
Tom Nook (Animal Forest - 2001)
Chibi-Robo (Chibi-Robo! - 2005)
Muddy (Mole Mania - 1996)
The Blue Virus (Dr. Mario - 1990)
Lip (Panel de Pon - 1995)
Furil (Nintendo Puzzle Collection: Panel de Pon - 2003)
Takamaru (Nazo no Murasamejou - 1986)
Harry the Robot (Teleroboxer - 1995)
Sukapon (Joy Mech Fight - 1993)
Donbe (Shin Oni ga Shima - 1987)
Ayumi Tachibana (Famicom Tantei Club Part II: Ushiro ni Tatsu Shoujo - 1989)*
Professor Kawashima (Brain Age: Train Your Brain in Minutes a Day - 2006)
Urban Fighters (Urban Champion - 1984)
#166 Golden Sun (2001) characters and/or Advance Wars (2001) infantrymen
#218 Famicom Tantei Club characters

Third Party Suggestions

Mega Man (Capcom) (Mega Man - 1987)
G-Red (Capcom) (Gotcha Force - 2003)
Simon Belmont (Konami) (Castlevania - 1986)
Power Pro-Kun (Konami) (Jikkyou Powerful Pro Yakyuu '94 - 1994)
Lupus (Rare) (Jet Force Gemini - 1999)
Sora (Square Enix, Inc.) (Kingdom Hearts: Chain of Memories - 2004)
Doctor Wright (Maxis) (SimCity - 1991)
Princess Katia (From Software) (Lost Kingdoms - 2002)
Kalas (tri-Crescendo/Monolith Soft) (Baten Kaitos: Eternal Wings and the Lost Ocean - 2003)
Magnus Gallant (Quest/Nintendo) (Ogre Battle 64: Person of Lordly Caliber - 2000)
Thomas the Kung-Fu Master (Irem) (Spartan X [Kung-Fu in the U.S.] - 1985)