Viewtiful Joe (GameCube version)
June 26, 2003
In the game there's a purchaseable power-up that lets Joe get bombs out of nowhere and juggle them. While doing so he whistles a part of the Super Mario Bros. ground theme, and it's actually a different part of it if it's done either on the ground, in mid-air or while in slow motion.
Capcom was licensed by Nintendo to produce a game on the GameCube, so they were able to include a little reference to the Mario series, but had to remove it when releasing the game on PlayStation 2.