Taken straight from official press documents: the list of 3DS titles in development.
Activision: DJ Hero 3D
AQ Interactive: cubic ninja
Atlus: Etrian Odyssey, Shin Megami Tensei (another main-series game?), Shin Megami Tensei: Persona (probably another port of the first game), Shin Megami Tensei: Devil Survivor (don't know if this will be a straight port of the DS game)
Capcom: Resident Evil Revelations, Super Street Fighter IV 3D Edition (tentative title) [!!!]
EA: FIFA Soccer, Madden NFL, The Sims 3
Gameloft: Asphalt GT
Harmonix: "Music game"
Hudson: Bomberman, Deca Sports, Kororinpa
Konami: "Baseball franchise," Contra, Frogger, Hideo Kojima's Metal Gear Solid Snake Eater 3D "The Naked Sample", Pro Evolution Soccer
Level-5: Professor Layton and the Mask of Miracle (tentative title)
Majesco: BloodRayne: The Shroud, A Boy and His Blob, Face Racers: Photo Finish, Lion's Pride: Adventures on the Serengeti, Martha Stewart, WonderWorld Amusement Park
Marvelous Entertainment: BOKUJYOUMONOGATARI 3D (tentative title; the real title will probably be Harvest Moon 3D)
Namco Bandai: Dragon Ball, Gundam, Pac-Man & Galaga, Ridge Racer, Super Robot Wars
Nintendo: Animal Crossing, Kid Icarus: Uprising, Mario Kart, nintendogs + cats, Paper Mario, PilotWings Resort, StarFox 64 3D, Steel Diver
Rocket: Crash-City GP, VS-robo
Sega: Sonic, Super Monkey Ball
Square Enix: Chocobo Racing 3D (codename), Dragon Quest, Final Fantasy, Kingdom Hearts
Take-Two: Carnival Games
Tecmo Koei: Dead or Alive 3D, Dynasty Warriors, Ninja Gaiden, Samurai Warriors 3D
Tomy: Lovely Lisa 3D, Naruto Shippuden Action
THQ: de Blob 2, Kung-Fu Panda Kaboom of Doom, Marvel Super Hero Squad Infinity Gauntlet, The Penguins of Madagascar, Puss N Boots, Saints Row: Drive-By
UbiSoft: Assassin's Creed: Lost Legacy, Battle of Giants: Dinosaur Strike, Driver: Renegade, Hollywood 61 (tentative), Tom Clancy'S Ghost Recon, Tom Clancy's Splinter Cell: Chaos Theory
Warner Bros: Batman, LEGO