Here is a list of hidden gems (and some not so hidden ones) that haven't been mentioned:
Claymates - Platformer
Flashback: The Quest for Identity - Action-Adventure
Marvel Super Heroes: War of the Gems - Beat-Em-Up
Metal Warriors - Action
Secret of Evermore - Action-RPG (One of my favorite SNES games)
Shadowrun - RPG (This one is somewhat hard to classify)
Troddlers - Puzzle-Platformer (Another one of my favorite SNES games)
Wild Guns - Shoot-Em-Up (This one is pretty unique, too)
X-Men: Mutant Apocalypse - Beat-Em-Up
Several of the best SNES games either have or will soon have ports/remakes on other systems, such as the DS, GCN, GBA, or Wii.
Oftentimes, they will have more content and/or a better price, so that's one thing to keep in mind if you own any of those systems.