I doubt I will really be able to give you anything off your radar, but GBA was the first game system I bought with my own McDonald's money, bought the GameCube later that year too. Although I didn't get an expansive library of titles for it, I played what I had a lot. Advance Wars and F-Zero: Maximum Velocity in particular I definitely put over 100 hours into each.
Don't have my SNES mini to play any GBA at the moment, handed it off to my nephew a few months ago, but I had some fun with loading up some stuff I had played way back when and trying a few new things I missed on the first go around.
I doubt Mario & Luigi Superstar Saga is overlooked, but I had never played it. Played through it start to finish, great Action RPG with some co-op puzzle style stuff to differentiate it from Super Mario RPG or Paper Mario.
bit Generations - Dotstream, I turned this one up on some list of games to try (hidden gems!) and I'm glad I did. It is simple looking race game and pretty darn tough, plus great music.
Kuru Kuru Kururin - possibly the first game I ever imported, either this or Doshin the Giant. Possibly from NCSX? I don't remember, but I bought the Australian version. A fun maze game, challenging but not overly so. Cutesy graphics, worth playing.
And not specifically GBA, but I still contend that with the right group Pac-Man Vs. is one of the greatest multiplayer party game experiences ever created.