Top 30 in no particular order
1. Golden Sun/Lost Age (probably the best RPG on the system and one of my favorites, great story, a great traditional battle system with incredibly epic summons that would put Final Fantasy to shame, great dungeon puzzles like Zelda, and a monster collecting element like Pokemon)
2 Metroid Fusion (An absolute masterpiece, and probably my favorite metroid game)
3 Castlevania Circle of the Moon/Aria of Sorrow/Harmony of Dissonence (not sure if each game should get its own spot or all share the same spot since they are all so similar, but they are all pure Metroidvania bliss, Aria of Sorrow is probably the best though)
4. Fire Emblem/ FE Sacred Stones (My favorite game series of all time, beautiful sprites and challenging gameplay, a terrific Strategy RPG)
5. Wario Ware/ Wario Ware Twisted (An awesome collection of silly short minigames, incredibly addictive and great for when you only have a few minutes to burn)
6 Final Fantasy Tactics Advance (I sunk over a hundred hours into this game back when it came out, absolutely incredibly addictive, can you believe I have not played the PS1 FF tactics? I need to remedy this)
7
8.
9 Pokemon Ruby/Sapphire/Emerald (how could it be a top GBA game list without Pokemon, and Gen 3 was the last great Pokemon generation imo)
10. Rythem Heaven Tengoku ( an excellent JP import, a collection of rhythm minigames much like Wario Ware)
11.
12.
13 Mario Golf Advance Tour (an excellent golf game on the little handheld made by Camelot, the makers of Golden Sun and Shining Force
14 Sonic Advance series (The last great 2D sonic games)
15. Advance Wars 1 and 2 (Another excellent Strategy game by the makers of Fire Emblem)
16.
17. Zelda Minish Cap (have not actually played this one yet but it comes with very high praise)
18
19. Drill Dozer (a great platformer made by the makers of Pokemon, Gamefreak)
20.Mario and Luigi Super Star Saga (a great simple RPG in the mario universe with a charming and humorous story)
21.
22.
23.
24. Mother 3 (an excellent RPG with a huge cult following)
25. Wario Land 4 (how could we not include this, an excellent platformer in the WL series and I think it was a launch game or very near launch)
26. Mario Kart Advance (do I really need to explain this?)
27. King of Fighters EX and EX2 (Surprisingly excellent SNK fighting game made just for the GBA)
28.
29. Tactics Ogre the Knights of Lodis (have not played it but had it recommended countless times)
30. Mario Vs Donkey Kong (a great little platformer, though I have only played a bit of it but its on everyones best of lists)
Honorable Mentions
So how does this list look? What should be replaced? and what should be honorable mentions?