I know most of these aren't actual Nintendo franchises, but I'd still love to see them.
TOAD 
Red and Blue from Contra.
Sonic, Knuckles, Tails, etc.
Aiai from Super Monkey Ball.
Axel, Blaze, Max, Skate, Dr. Zan from Streets Of Rage.
Bubsy
Earthworm Jim
Frog/Glenn
Angel from Actraiser
B.O.B.