Being a big fan of F-Zero, the F-Zero series would probably be my first choice... Maximum Velocity was average, but GP Legend and Climax were both awesome games.
Other than F-Zero, Golden Sun would get my vote too, the first game was mindblowing, it really showed what the GBA was capable of.
Advance Wars and Fire Emblem would both come a joint second/third on my list... I'm not a massive SRPG fan but these games really ate up a lot of gaming time.
Mario Tennis and Golf are also worth mentioning, they were very good games. And of course Wario Ware, dam that game was crazy!
Loads of other games had an impact on me too... remember playing V-Rally 3? I had trouble believing something like that was even possible on the GBA! Heck it has better visuals than some DS games lol. Megaman Battle Network was great back in the day too, shame Capcom ruined it. Hmm... so many good games (and quite a few stinkers!).
=)