In no particular order:
LoZ:OoT3D (3DS)
Pushmo (3DS eshop)
999 (DS)
The World Ends with You (DS)
Chronotrigger (DS)
Super Mario 3D Land (3DS)
Tales of the Abyss (3DS)
Ghost Recon: Shadow Wars (3DS)
Nano Assault (3DS) (but only if you don't mind DIFFICULT)
Professor Layton series (DS so far)
Phoenix Wright: Ace Attorney (DS)
Cave Story 3D (3DS)
Shin Megami tensei: Devil Survivor Overclocked (3DS)
Tetris Axis (3DS)
That's just the tip of the iceberg though for the DS, and for the 3DS there are lots of good things coming on the horizon.
Currently Playing: Shin Megami Tensei: Devil Survivor Overclocked, Professor Layton and the Curious Village
Anticipating: Xenoblade, The Last Story, Mario Kart 7, Rayman Origins, Zelda SS, Crush3D, Tales of the Abyss 3DS, MGS:Snake Eater 3DS, RE:Revelations, Time Travellers, Professor Layton vs. Ace Attorney, Luigi's Mansion 2, MH TriG, DQ Monsters, Heroes of Ruin
