Ninja 5-0 and Drill Dozer stick longest in the memory.
Most of the Bit Generations puzzlers were quality. Digidrive in particular.
Warioware Twisted and Rhythm Tengoku hold a special, mad, place for me.
AstroBoy: The Omega Factor was an incredible achievement by Treasure.
And of course, the two Metroid games, particularly Zero Mission.
Oh, and Racing Gears Advanced.
Dmanit - Advance Wars and it's sequel - And that mini X-com game - And TMNT - And Ghost Rider...
Too many great games on GBA