1ST Kid Icarus: Uprising- If you got a problem with the controls, you're a bitch. The online is a blast, the gameplay ferocious and fun, and the story is lovingly crafted- plus, the game utilizes pretty much every 3DS function in some way, which is awesome. Overall, it seems like one of the only titles really BUILT for the 3DS, and it's an immensely entertaining ride.
2ND Resident Evil: Revelations- Yeah, this game is boss. As my first foray into the Resident Evil saga, I could not have chosen a better title, mixing the formula of the old with a little bit of the new. Immensely fun online co-op and single player raid mode, and a beautiful, atmospheric single-player campaign. Seriously, do yourself a favor and GET IT. Also, DAT CIRCLE PAD PRO!
3RD (TIE) Mighty Switch Force and Mutant Mudds- Both titles are lengthy, gorgeous romps for the eShop. Great mechanics are implemented in both, and Mighty Switch Force goes for however much mileage you get out of the title with its Par Times and difficult, but wonderfully appreciated DLC, and Mutant Mudds goes for being balls-to-the-walls tough with precision platforming and interesting level design (including 3D perspective plane jumping).
I refuse to include Ocarina, as it was mostly boring, and that atrocity known as Super Mario 3D Land was a summation of everything I hate about where the franchise has been heading in recent years.