I haven't played a ton of it, but Avenging Spirit is a GB game that hasn't been mentioned here but deserves to be in a discussion of best games on the system.
But Link's Awakening is my overall pick. It's maybe the game most responsible for my love of games in general. Before it, I had mostly just watched my dad and cousins play NES/SNES games. But Link's Awakening was my own adventure. And a huge and trippy adventure, to boot!