Oh bloody hell, let me think.
Wind Waker - Twice on Gamecube (standard and special editions), once on Wii U = Total of 3.
Kirby Fun Pak/Super Star - Once on SNES, once on Wii U eShop, once on DS, once on Switch (NSO) = Total of 4
Ocarina of Time - Once on N64, twice on GameCube, once on 3DS...