Definitely A Link Between Worlds for me, which was a wonderful return to form after the dreadful DS games. My other top games would be Mario Kart 7 and Super Mario 3D Land. The Star Fox and Zelda remakes were nice too and it certainly had some good games (Dark Moon, RE Revelations, Smash, etc).
All in all though, 3DS is not one of my favorite Nintendo systems. Other than maybe some Picross/3D, I don't think I've played a game on it since well before Switch came out.