I don't have very many (since I never had a GBA -- just a DS), so my choices are somewhat predictable:

FFTA
Advance Wars 2
Golden Sun
Fire Emblem

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The Castlevanias: Aria of Sorrow is mandatory, no excuses. Circle of the Moon is a also a must. And Harmony of Dissonance... although that last one it's not as good as the others IMHO.

There is also the Castlevania Double Pack that includes AoS and HoD in the same cart, which is neat. Only thing I don't like about the Double Pack is that you can't use it to unlock the Mina Doll and start with a Rare Ring in Dawn of Sorrow; only the AoS cart works for that.

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I used to have a bunch of gba games...but I slowly even up selling them for a quick buck (which I now regret).
My faves would have to be the first and second Golden Sun, Metroid Fusion and Zero Mission (even tho I could never beat the original nes game, guess I suck...) and Fire Emblem (6?). I should also put Mario Kart in that list since it did keep me awake during spanish class in H.S and the Super Mario Advance series (of which I still have the 4th one, SMB3 :3).

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Golden Sun :)

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I never had a GBA, only a DS, so I only have a couple. There's a Spyro one I like, as well as Harvest Moon FoMT.

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I only bought one GBA game for my DS so far: Counter punch. I like it as much to keep the dust out as I do for the actual game play.

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Gunstar Super Heroes is essential and it still hasn't left my GBA slot since the game was released. Which will be something like 3 years coming this fall.

(Sure, I haven't played it all the time during those years, but it's still fun every time I play it)

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Castlevania: Aria of Sorrow
Kirby and the Amazing Mirror
Metroid Fusion
Mario & Luigi: Superstar Saga
Advance Wars
Astro Boy: Omega Factor
Wario Ware: Twisted
Final Fantasy VI
The Legend of Zelda: The Minish Cap
Golden Sun
Mario Kart Super Circuit
Super Mario Advance: Yoshi's Island
Gunstar Super Heroes
Sonic Advance 2
Castlevania: Circle of the Moon
Super Ghouls and Ghosts
Metal Slug Advance
Wario Land 4
Donkey Kong Country
Super Puzzle Fighter II
Drill Dozer

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by far the greatest gba game series out there is golden sun and lost age

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Metroid Fusion and Zero Mission
Astro Boy Omega Factor
Mario and Luigi Superstar Saga
Advance Wars 1 and 2
Golden Sun 1 and 2
WarioWare Inc
Zelda The Minnish Cap
Castlevania Aria of Sorrow and Circle of the Moon
Final Fantasy Tactics Advance
Riviera
Gunstar Super Heroes

The GBA is probably the only system that I've consistently finished the games during it's lifetime. I'm currently still finishing PSX and PS2 games, and I'm not even close to finishing Mass Effect and Ace Combat 6 for my 360 yet ^_^;

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Golden Sun Series.

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Metriod Fusion & Zero Mission
FFTA (logged over 100 hours)
Zelda: Minish Cap
Castlevania: Circle of the Moon, Harmony of Dissonance, Aria of Sorrow
Astro Boy
Gunstar Super Heroes (currently trying to beat on hard mode)
Metal Slug
Bookworm (so damn addictive)
Tactics Ogre
Advanced Wars 2
Any / All of the Mario re-makes

Damn....I still play my micro every day!!!

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I only have Sword of Mana and Pokemon LeafGreen, since, like others, I missed out on the GBA. I'll have to try and find some of these~

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WarioWare Mega Microgame$
Advance Wars
Legend of Zelda: The Minish Cap
Mario & Luigi: Superstar Saga
Final Fantasy Tactics Advance

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Sonic Advance 3... but it got burnt in the toaster by my bratty brother (it lives on as a Visualboy ROM) and Pokémon Emerald. Fire Red was pretty good, too, but ended up with my sister and her level 96 Charizard named Chazze (which was traded to Emerald but I started a new save... whoops) He lives on in Pokésav. And... Yu-Gi-Oh world Tournament 2004 and the Sacred Cards. Also, although I never owned it, the Minish Cap was a once in a while treat.

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