The World Ends With You - Not a typical RPG that has a system that uses the DS controls, quirky storyline, and one of the best soundtracks from an RPG I've heard in years (presupposing you like J-Pop/Hip-Hop stuff). Probably one of the best DS games I've ever played.
Shin Megami Tensei: Devil Survivor - It's MegaTen! As an SRPG!
Shin Megami Tensei: Persona - If you are looking for something a little old school, this game is a remake of a PS1 game from the mid-90's. A quirky plot, some laughable dialogue (though infinitely better than the original), multiple endings and even an alternate storyline to play through with its own ending.
Digimon World Dusk/Dawn - Pretty solid RPG with a deep customization growth system that is very similar to the Disgaea games. The stories not half bad but the real joy is just raising your army of Digimon.
Sword of Mana - Remake of FF Adventures, good music, great action-RPG combat and a good story. Two different heroes to play through (Play the girl first) and its smurfing Seiken Denetsu.
Half Minute Hero - Not a typical RPG... but its still fun (and funny) as hell. Of anything, download the demo off PSN.
Kingdom Hearts 358/2 - Combat takes awhile to adjust to but overall, I really enjoyed the game and I liked the story (though to warn you, I'm a whore for Roxas and Org. XIII). Lots of extra challenges make redoing missions pretty fun and there is s bit of variety as well so its not just combat.
Valkyrie Chronicles - Though I personally have some issues with the game, the combat and puzzles are fun as hell and the game has a large cast to play as. Not to mention Multiple endings.
Star Ocean 1 + 2 - Great combat and characters, stories are bit... odd but fun none the less. Star Ocean 2 is pretty damn awesome has a great crafting system and fun mini-games.
Rhapsody: A Musical RPG - Its by the same people who do the Disgaea games. The music is either laughable, cute or downright catchy. Story is hilarious.
I will think of a few more later.