My favorite game on 3DS is Mario 3D Land. Somehow the game beats the Wii U version due to being truly optimized for one player and I was happy to see Mario ditch the Galaxy theme.
Pokemon is always a time sucker, that game is something I am embarassed to say I really enjoy.
The Nintendo catalog in general is solid. Luigi's Mansion and DK Country also really stand out. Other good titles were Mario Kart, Fire Emblem, Pushmo, and Professor Layton.
Non-Nintendo games can be fun, but obviously arent the system seller. Shinobi was a game mentioned recently I enjoyed. Hell, I even downloaded and played a decent amount of Game Gear Shinobi from the 3DS Shop.