Here are my tops:
Golden Sun 1 and 2
Mother 3
Advance Wars 1 and 2
Final Fantasy 5
Final Fantasy 6
Final Fantasy Tactics Advance
Dragon Quest Monsters Caravan Heart
Megaman Battle Network Series
Castlevania Series
Dragon Ball Z : Legacy of Goku 1-3
Fire Emblems
Kirby Nightmare in Dreamland
Mario and Luigi
Legend of Zelda : Minish Cap and Link to the Past
Mario Tennis
Metroid Zero Mission, and Fusion
Phantasy Star Collection
Shining Force
Sword of Mana
Pokemon FireRed, and Emerald
Lunar Legends
Super Mario Advance: Super Mario World, Yoshis Island, and Mario Bros. 3