Emphatically agreeing with several of the above posters: Golden Sun! Boktai! Also Final Fantasy Dawn of Souls (I, II), V, VI Castlevania- Harmony of Dissonance, Aria of Sorrow (Circle of the Moon is decent, but not a fan of the main character's sprite) Kingdom Hearts: Chain of Memories (yeah, some people don't like it, but I found it fun- though tricky to play)
My favorite GBA game would have to be Hamtaro: Ham-Ham Heartbreak, although Mario & Luigi: Superstar Saga is a close second.
Aside from the Pokemon games, the Golden Sun games. Then there's the Tales of Phantasia port, as well as the Fire Emblem games. Then the GBA port of Lunar: Silver Star Story and although not as great as the first two, the third game in the Lufia series.
Aside from Pokemon and Breath of Fire, I have to go with Megaman Battle Network Version 3 Blue. I love the Megaman Battle Network series and version 3 was the first one I played so it has a special place in my heart. XD
I always found it interesting that Super Mario Bros. 2 was originally released in Japan as a followup to the first game. By that I mean, the gameplay was the same, graphically it was the same game but the levels were all different and much harder. Nintendo of America figured the game to be too difficult and wasn't innovative enough to satisfy a North American consumer so they licenced a game called Doki Doki Panic which featured some Arabian style characters. The changed the sprites and nobody was the wiser. It also explains the wildly different gameplay than previous and subsequent Super Mario games. It was so popular that it was released in Japan as Super Mario USA. The original Japanese version of the game later got bundled into Super Mario All Stars for the SNES which is a neat look at what could have been. I'm happy things worked out the way they did though because Super Mario Bros. 2 was loads of fun. Anyway, favourite GBA game. It's been so long since I played it but I would probably say Advanced Wars or maybe the Super Mario World remake. I never did try Golden Sun. For whatever reason, despite the rave reviews, I never picked it up and never played it. My brother had it and loved it. One of these days I'll either buy a used copy or borrow his and play it.
Since I only own Pokemon Emerald, Leaf Green, and PMD: Red Rescue Team... Emerald and PMD: red I cried with the PMD game. Twice. Because I accidentally delete my save once.
Fire Emblem!!!!<333 I love love love love love love love them. Others that meet the list: Metroid Fusion Pokemon
Hmm it would have to be The Legend of Zelda: The Minish Cap. Or TLOZ: Four Swords. But also Pokemon Emerald.
played mario golf the most huge pokemon fan, though i skipped the advanced part of pokemon then when back to it otherwise would be pokemon for all other gameboy systems