Okay, let's first list all possible third party developers. I might update this list later on, but right now it seems very hard to come up with any character right now.
The ones already in:
Konami (Snake)
Sega (Sonic)
Capcom (Mega Man)
The ones that are a possibility:
Namco Bandai
One of the three forces behind the Triforce arcade board. Aside from that, they have made some Nintendo exclusive games, like Star Fox: Assault and the Donkey Konga series.
Notable characters that have appeared on a Nintendo console
Pac-Man
Lloyd Irving
Klonoa
KOS-MOS
Square-Enix
Had most of its early library on Nintendo consoles. They made several exclusives, including the Final Fantasy: Crystal Chronicle series, Super Mario RPG and Mario Hoops 3 on 3.
Notable characters that have appeared on a Nintendo console
Black Mage
Chocobo
Moogle
Randi (male protagonist of the Secret of Mana, unconfirmed name)
Slime
Treasure
Made various Nintendo exclusives, and is probably best known for games like Gunstar Heroes, Mischief Makers and Sin and Punishment.
Notable characters that have appeared on a Nintendo console
Marina Liteyears
Marvelous Entertainment
Best known for games like Harvest Moon. Mostly acts as a publisher.
Notable characters that have appeared on a Nintendo console
Travis Touchdown (debatable: it was only published by Marvelous Entertainment in Japan)
Ubisoft
Known best for its mascot Rayman.
Notable characters that have appeared on a Nintendo console
Rayman
Travis Touchdown (debatable: it was only published by Ubisoft in North America)
Jade (Beyond Good & Evil)
Tecmo Koei
Was mostly only active on the older Nintendo consoles on the Tecmo side, now their releases on Nintendo consoles are very limited. Best known for the Ninja Gaiden series.
Notable characters that have appeared on a Nintendo console
Ryu Hayabusa
Companies that are now most likely out of the question
Hudson Soft
Hudson Soft currently is owned by Konami, so any character falling under Hudson Soft now effectively falls under Konami as of 2003.
Rare
Rare is owned by Microsoft, therefore eliminating Rare.
Characters which are really fucking hard to identify the owning company for
Spyro the Dragon - Went trough several developers and publishers.
The ones already in:
Konami (Snake)
Sega (Sonic)
Capcom (Mega Man)
The ones that are a possibility:
Namco Bandai
One of the three forces behind the Triforce arcade board. Aside from that, they have made some Nintendo exclusive games, like Star Fox: Assault and the Donkey Konga series.
Notable characters that have appeared on a Nintendo console
Pac-Man
Lloyd Irving
Klonoa
KOS-MOS
Square-Enix
Had most of its early library on Nintendo consoles. They made several exclusives, including the Final Fantasy: Crystal Chronicle series, Super Mario RPG and Mario Hoops 3 on 3.
Notable characters that have appeared on a Nintendo console
Black Mage
Chocobo
Moogle
Randi (male protagonist of the Secret of Mana, unconfirmed name)
Slime
Treasure
Made various Nintendo exclusives, and is probably best known for games like Gunstar Heroes, Mischief Makers and Sin and Punishment.
Notable characters that have appeared on a Nintendo console
Marina Liteyears
Marvelous Entertainment
Best known for games like Harvest Moon. Mostly acts as a publisher.
Notable characters that have appeared on a Nintendo console
Travis Touchdown (debatable: it was only published by Marvelous Entertainment in Japan)
Ubisoft
Known best for its mascot Rayman.
Notable characters that have appeared on a Nintendo console
Rayman
Travis Touchdown (debatable: it was only published by Ubisoft in North America)
Jade (Beyond Good & Evil)
Tecmo Koei
Was mostly only active on the older Nintendo consoles on the Tecmo side, now their releases on Nintendo consoles are very limited. Best known for the Ninja Gaiden series.
Notable characters that have appeared on a Nintendo console
Ryu Hayabusa
Companies that are now most likely out of the question
Hudson Soft
Hudson Soft currently is owned by Konami, so any character falling under Hudson Soft now effectively falls under Konami as of 2003.
Rare
Rare is owned by Microsoft, therefore eliminating Rare.
Characters which are really fucking hard to identify the owning company for
Spyro the Dragon - Went trough several developers and publishers.