My favourite so far is Kid Icarus Uprising, which is in my top3 favourite games I played this year. The one I played the most though is Theathrythm FF... I was addicted to it during summer vacation, playing everyday.
The best game is Virtue's Last Reward, the sequel to 999. It's improved in nearly every way.
I'm very inclined to agree, since I loved VLR and 999 both, but the glitches in that game are the only thing holding it back from "Best 3DS game" status. Once Chunsoft and Aksys patch it up, it'll be officially the best.
For now, I'm really wanting to say Kid Icarus or Ocarina of Time 3D. Both are excellent games! KI has controls that take time to get used to, but it's not a deal-breaker by any standard.
Tales of the Abyss. There's no other 3DS game that you will spend as much time on the single-player. Mario Kart 7 or Kid Icarus if you want to spend a majority of the time online, I recommend the latter. Mario Kart gets old fast.