Probably played Advance Wars more than anything else on GBA. Highly recommended if you like turn based strategy games. Fire Emblem is good too, but AW has less story and you don't have to deal with permadeath. More conducive to quick games on the go.
Metroid Zero Mission is great, and so is Fusion.
The first Wario Ware is the best Wario Ware.
Scourge: Hive is kinda like Metroid in an isometric perspective.
Lord of the Rings: Return of the King is like Diablo in Middle Earth.
Gunstar Super Heroes is a fantastic run and gun shooter that pushes the GBA hardware as far as it can possibly go. Astro Boy: Omega Factor is pretty similar. Both made by Treasure.