My GBA Favorites (aka: Teh Best! ):

Castlevania Series (Circle, Aria, and Harmony)
Mario & Luigi (I'm not much of an RPG fan, but I couldn't stop playing this gem)
Sonic Advance Series (Reminded me of the Genesis days of old)
Super Mario Advance Series (Each one is a classic)
Metroid Zero Mission

Golden Sun 1 and 2
FF IV
Pokemon Emerald
Pokemon Firered/leafgreen
X2 [i liked it....]

EDIT: Oh, and Minish Cap! Can't forget that.

EDIT #: Sonic Advanced Series!!!

Ninja Five-O is my favorite..... if you have not played this you are missing out.
Very hard to find, but well worth whatever amount you have to pay to get it.

The rest of my top ten.....

Legend of Zelda Link to The Past
Super Mario Advance 4 (Super Mario 3)
Wario Land 4
Kim Possible 2: Drakken's Demise
Kirby & The Amazing Mirror
Metroid Fusion
Wario Ware Twisted
Super Mario Advance 3 (Yoshi's Island)
Mario vs. Donkey Kong

Golden Sun (both). They're the best (non port) GBA games, imo.

Pokemon Emerald Sapphire Leaf Green

I have yet to play a good Game Boy Advance game.
I hope I will.
I'll certainly try Metroid Fusion one of these days.

Megaman Battle Network 1-3 were awesome for me. I loved Zero series as well. Picking games that weren't said.

Mother 3.

If only I could read it.

The legend of zelda minish cap.
Yoshi's Island.

I can't believe no one said Klonoa yet.