There were a few really good third-party 3DS games.
Heroes of Ruin
Do you like the Diablo series on PC? Do you like the concept of StreetPass, SpotPass, and 3DS online? Then this game is basically made for you. n-Space and Square Enix are teaming up to bring a large class-based dungeon crawler to Nintendo's new handheld with great graphics, fun gameplay, and randomized levels. Throw in the potential of support for the 3DS' various connectivity features, and Heroes of Ruin might be the most exciting third-party title on the system. Read our impressions for more details.
Honorable Mention:
Resident Evil: Revelations, Nano Assault, Shinobi, Mutant Mudds