The absolute best DS game I've ever played is rune Factory 3. the story was great, the gameplay was CRAZY addictive, the characters were fun and engaging. It's like combining all of the best aspects of Harvest Moon, Legend of Zelda, and Final Fantasy in one single game. Just perfect.
Every Ouendan game, including Elite Beat Agents... Now THOSE were amazing.
Dawn of Sorrow was so very enjoyable, too. I rather enjoyed Portrait of Ruin as well, though I don't think a lot of others did.
Blue Rescue Team is probably my second-favorite RPG storyline... maybe even my first. It's hard to say.
Drawn to Life was surprisingly enjoyable, even if it was simplistic.
Sonic Rush had some cool stages, too.
And finally, I still have to finish Dragon Quest IX at some point. =P