Bravely Default is the best Final Fantasy game in years. It's not perfect, but it's amazing. And the sequel's coming out in April.
Etrian Odyssey (a series of hardcore retro dungeon crawlers) has three great 3DS installments: Etrian Odyssey IV, Etrian Odyssey Untold, and Etrian Odyssey 2 Untold. The latter two are remakes of the first two games, originally for the DS. The series is very love-it-or-hate-it (I am in the "love it" camp), so try one of the demos first.
Fire Emblem Awakening and Fire Emblem Fates are great strategy RPGs.
Kid Icarus: Uprising is a lot of fun once you get used to the awkward controls.
Kingdom Hearts 3D: Dream Drop Distance, though only if you've played the series before and liked it, since the story here falls pretty hard into continuity lockout. Not the best installment, but still a lot of fun.
Kirby Triple Deluxe feels like an expansion pack for Kirby's Return to Dream Land, but seeing how RtDL is the best Kirby game yet (in my opinion), this is not a bad thing.
The Legend of Zelda: Ocarina of Time 3D and Majora's Mask 3D. Exactly what it says on the tin.
Pokemon X/Y and Pokemon Omega Ruby/Alpha Sapphire. Freaking duh.
Shin Megami Tensei: Devil Summoner - Soul Hackers, Shin Megami Tensei: Devil Survivor Overclocked, Shin Megami Tensei: Devil Survivor 2 - Record Breaker, and Shin Megami Tensei IV. In order: remake of an old Japan-only Sega Saturn/PlayStation RPG, two enhanced ports of DS strategy RPGs, and an awesome RPG made for the 3DS. Devil Survivor 1 in particular will really appeal to you if you like Pokemon, since it's a deconstruction of the concept (basically it answers the question "What would happen if Pokemon suddenly appeared in the real world?" and needless to say things don't go well).
StarFox 64 3D
Super Mario 3D Land is a ton of fun.
Tales of the Abyss, if you never played it on PS2.
Theatrhythm Final Fantasy: Curtain Call might be the most content-rich rhythm game ever made, with well over 200 songs included before you even get into the DLC. And the RPG elements, with party-building, leveling, and customization kept me at least coming back to it over and over. I have clocked over a hundred hours into this beast, and I do not regret a cent of the money I spent to get every piece of DLC released for it.
That's... almost every game I have for my 3DS, actually. Not counting eShop games.