Advance Wars (and it's Sequel) are great.
Wario Ware is awesome. Just take 10 seconds and you'll be hooked.
Mario vs Donkey Kong
As stated before: Metroid Fusion and Metroid: Zero Mission are grand
Also stated before: Castlevania: Circle of the Moon, Harmony of Dissonance, and Aria of Sorrow are all great.
If you like Strat RPGs, the Super Robot Taise: Original Generation (1 and 2) are great...
In fact: You can count on these games that were put out by Atlus to be great:
Super Dodge Ball Advance
Super Double Dragon
River City Ransom EX
Amongst many, many others.
There are a lot of quality games on the GBA. Hell, Nintendo needed their portable platforms to carry the weight of their waning home consoles at the time, and the GBA acted like Atlas holding up their existence for a while.