This one may be a bit of a stretch since it's not sequential, but the original Donkey Kong has gone through quite a few retail releases, even though some haven't been on Nintendo platforms! After its arcade release, it had retail versions on the Colecovision, Intellivision, and Atari 2600. After the NES version, it was also sold at retail for the e-Reader and on the GBA as part of the Classic NES Series. It even had a Game and Watch version! This isn't even counting Donkey Kong 64 and Animal Crossing, since they're their own games that just happen to feature the original Donkey Kong.
The first Donkey Kong Country had a few retail versions too; one on the SNES, one on GBC, and one on GBA.
Edit: Looks like my second example was beaten by a second.