Pokemon x/y (Super amazing. You can walk diagonally, sit down, have roller skates..Its just too much fun)
Mario Kart 7 (Borrowed, but super fun. Even better with friends)
Animal Crossing New Leaf (Never played, heard it was fun from friend)
Fire Emblem (Never played, heard it was good. If you like strategy games that is)
Legend of Zelda Link Between Worlds (Brother loves this game. Sadly he doesn't have a 3ds nor money)
I sadly just took someone else's list and put some of my opinions.
I prioritized Kingdom Hearts, Fire Emblem, Professor Layton, and FF Theatrhythm.
Theatrhythm is a rhythm game, which you might not be into. Professor Layton is a puzzle game which was really fun for me.
Fire Emblem is a really fun strategy RPG, and has a really good storyline and gameplay. After you finish the game, you can keep training characters or challenging yourself with DLCs.
Kingdom Hearts 3D is REALLY underrated. I don't expect games like these to be really popular, but no one that I know has a 3DS plays it, or even has considered playing it. The action gameplay is very fun and the abilities and storyline are amazing.
Other games I've considered, but not bought yet or haven't been released, are Super Smash Bros, Kirby Triple Deluxe, Bravely Default (basically has Final Fantasy gameplay, with an extra battle system), and Legend of Zelda.