NES: Mario 3
SNES: TMNT 4: Turtles in Time, Mario World, A link to the past, etc.
N64: Mario 64, Majora's Mask, OOT 64.
Gamecube: Mario Sunshine, F-Zero GX.
Wii: Mario Galaxy Series, the various "Wii" line of games and Mario Kart Wii.
Obviously I have more to list or some wanting to beat so I'll keep this post updated.