Golden Sun and Golden Sun The Lost Age. I flatly refuse to pick between one or the other. They are like two perfect halves of the same masterpiece and are some of the best games I have ever played regardless of system.
But really, are there too many spectacular GBA games or what? Not too many obviously, but the system is just FULL of shining gems. Others I can think of without even trying include Astro Boy, Mario and Luigi, Mother 3, Castlevania AOS, Zelda Minish Cap, Metroid Fusion, Metroid Zero Mission, DBZ LOG 2 and Buu's Fury, Gunstar Super Heroes, MMBN 1-3, Boktai 1-3, Kingdom Hearts COM, and Mario VS Donkey Kong. Those are just games I can think offhand. There are just so many great ones.