Mine is Fire Emblem: Awakening!
But I also really liked New Leaf, Ocarina of Time 3D and Kid Icarus: Uprising
My favourite 3DS game is Virtue's Last Reward because it truly has the number #1 greatest story of any video game ever made (the second best story is from its predecessor, 999: 9 Hours, 9 Persons, 9 Doors) and it's just so freaking incredible and I bloody despise the fact that nobody has heard of it.
I want to play 999 but it isn't out in Europe
I might actually get hold of Virtue's last reward