Some great suggestions... a couple more:
* Revenge of the Gator (pinball)
* Monster Max (by the legendary John Ritman. Liked Head Over Heels? Get this)
* Mario Picross 2 (an excellent puzzle game, like chipping away at a picture -- if you're using an emulator, there's a translated ROM).
* Warioland 1, 2, 3 (as good as Mario Land, perhaps even better)
* Batman (old, but perfectly done)
* Metroid 2 (not as good as the first, but still great)
* Dropzone (perfect conversion from the c64)
* Mystic Quest (prequel to Secret of Mana -- AWESOME Action-RPG)
* Deja vu (good adventure game)
* Donkey Kong 94 (adds a *lot* to the original, improving playability enormously)
* Harvest Moon (mixture of RPG & farm sim)
Most of the Final Fantasy Legend titles were top-notch, and there was a good Kirby platformer (can't remember the title)
Don't forget the two newer Zelda games, Oracle of Ages and Oracle of Seasons.
Oh, and surprisingly, the Tomb Raider game was actually pretty good on GBC! More like Prince of Persia.
Plenty more good titles...