I can't believe no one has mentioned SMW2: Yoshi's Island. I guess it came on the tail end of the system, when the 32-bit systems came out, but it remains the greatest platformer of all time. Too bad not enough people played it, since nothing has come close since.
If I only had one choice, that would get my vote, but secret of mana, super metroid, and a link to the past get honorable mentions. Although I could write a VERY long list of SNES games that are worthy of recognition. It really was the greatest system ever.