My favorites.
Shining Soul one and two: plays more like an MMORPG without the massiveness. Multiplayer goes up to four players, and thats where the game actually gets good as things change some with more players and some cooperation.
Summon Night Craft lord: found it just plain fun. Its more dungeon like and you dont do alot of the exploring you do in most RPGs, but its fun to make weapons and fight all Tales of Phatasia style without the semi-auto hting in the way. [The sequals are better, but theres no word of them coming to the US. I do hope someone translates them :3 They have more exploring in them it seems.]
Breath of Fire one and two are some nice ports, but somehow I feel like the SNES version was more worth playing despite the small updates in the GBA version.
Keitai Denjuu Telefang 2: a thick japanese pokemon alternitive. They made a game for GBC in english called POKEMON diamond or something. Ive found it interesting a bit.
Phantasy Star 1 2 and 3 were ported to the GBA too.
RPG Tsukuru Advance: RPG maker (pointless but worth mention)
DemiKids Light and Dark versions: Another pokemon like game but with a fairly interesting story.
The japanese Full Metal Alchemist RPG was fun, but its all in japanese ofcourse.
Kingdom Hearts Chain of memories.: didnt get the story, but it was a fun yet odd card like game. Its worth a try atleast.
Rivera: Loved this one. Story is intriging and it has a big stradegy elemnt to go with it. Though alot of times your going around the same backgrounds but going through differnt areas anyway. Its confusing, but has an interesting system. Worth a few trys. (I suggest you use save states though, ya never know what might happen in the game sometimes)