I'm just realizing this is missing some titles. I'll edit it soon, hopefully.
The Amazing Spider-Man
Angry Birds Star Wars
Angry Birds Trilogy (cart only)
Battleship
Bravely Default
Bit Trip Saga
Chibi-Robo: Zip Lash (Amiibo box set)
Codename: S.T.E.A.M.
Code of Princess (+cart only)
Cubic Ninja
Cut the Rope Triple Pack
Doctor Lautrec and the Forgotten Knights
Donkey Kong Country Returns 3D
Dream Trigger 3D
Epic Mickey Power of Illusion
Fire Emblem: Awakening
Fire Emblem Warriors
Ghost Recon: Shadow Wars
Kid Icarus: Uprising (Box set with stand)
Kingdom Hearts 3D (cart only)
Kirby: Triple Deluxe
The Legend of Legacy
The Legend of Zelda: Ocarina of Time 3D
The Legend of Zelda: Tri-Force Heroes
The Legend of Zelda: Majora's Mask 3D
LEGO Jurassic World (cart only)
LEGO The Lord of the Rings
LEGO Marvel Avengers (cart only)
Luigi's Mansion: Dark Moon
Madden Football
Megaman Legacy Collection (Amiibo box)
Metroid: Samus Returns
Metroid: Samus Returns
Monster Hunter IV Ultimate (cart only)
Monster Hunter: Generations
Nickelodeon Nicktoons MLB 3D
Paper Mario: Sticker Star
Pilotwings Resort
Pokémon Moon (cart only)
Poochy and Yoshi's Wooly World
Poochy and Yoshi's Wooly World
Professor Layton and the Miracle Mask
Rayman 3D
Reel Fishing: Paradise 3D
Rhythm Thief & the Emperor's Treasure
Rhythm Thief & the Emperor's Treasure
River City: Tokyo Rumble (w/ keychain)
Samurai Warriors: Chronicles
Scribblenauts Unmasked
Scribblenauts Unmasked
Sega 3D Classics Collection
Shin Megami Tensei IV (cart only)
Shinobi
Sonic All-Stars Racing Transformed
StarFox 64 3D
Steel Diver
Stella Glow (Launch edition big box)
Super Mario Maker
Super Smash Bros. 3DS (+cart only)
Sushido: The Way of the Sushi Striker
Takes of the Abyss
Tetris: Axis
Ultimate NES Remix
Virtue's Last Reward
Xenoblade Chronicles 3D
Yokai Watch 2: Fleshy Souls
Yoshi's New Island