That depends on taste, and what game genre you enjoy the most. I guess.
Personally one of my favourite GBA games ever is Castlevania Aria of Sorrow. I also like the ports for FF IV, V and VI, but I don’t know if that counts much since they’re updated ports. But they do have tons of extras so…
Among a legion of Mario and Pikachu fans, there wasn’t much room for me in the GBA world aside from the role playing games, remakes and originals.
Also I’ve yet to find Castlevania Circle of the Moon which I totally want.
I guess we can add Harmony of Dissonance to my list, since Castlevania owns, although that’s by far not one of my fave Castlevania games.