1st) Luigi's Mansion: Dark Moon
Best multiplayer, best action game.
2nd) Zero Escape: Virtue's Last Reward
Everyone should play this and Nine Hours, Nine Persons, Nine Doors.
3rd) Animal Crossing: New Leaf
Brilliantly executed, hundreds of hours clocked in, still a lot to collect.
4th) The Legend Of Zelda: A Link Between Worlds
Majora's Mask is my favorite Zelda game but I haven't played it on the 3DS yet... it's in the backlog though!
5th) Bravely Default
Best RPG. Great characters, great job and battle systems.