3DS? Don't you mean the Etrian Odyssey Machine?
Etrian Odyssey IV, Etrian Odyssey V, Etrian Odyssey Nexus, Etrian Odyssey Untold 1, Etrian Odyssey Untold 2, Persona Q, Persona Q2.
...fine, have some non-Etrian games too.
Picross 3D Round 2 is a must for anyone with an interest in puzzle games. By the end you'll lament the fact there will never be a Round 3. Back to 2D picross forever. :(
Gotta Protectors might be the most underrated game on the system. Think Gauntlet + tower defense with extra depth and a ton of personality. It's even better with a friend or two.
Monster Hunter 4 Ultimate is arguably the peak of the series. I personally like Generations Ultimate slightly more but you can't go wrong with 4U.
Mario Golf World Tour is the best entry in its series as well. With the DLC courses you have over double the holes any other Mario Golf can offer and they all play perfectly.
Poochy and Yoshi's Wooly World is a rare case of the downgraded port being superior to the original. Also the 30 or so stop-motion animated shorts are adorable.
All of the Sega 3D classics are amazing renditions of the original games. M2 did a superb job with the ports.
Every year I come closer to the realization that the 3DS might be my all-time favorite system. There's just so many quality games.