Ubisoft have six Nintendo 3DS games in development. Four of these are known franchises from the company: Assassin’s Creed: Lost Legacy, a remake of Tom Clancy’s Splinter Cell: Chaos Theory, Tom Clancy’s Ghost Recon and Driver: Renegade.
The other two are newer I.P. One is a brand new franchise named Hollywood 61 and is described as an interactive 3D movie. The other is Battle of Giants: Dinosaur Strike. You can find screenshots here.
In addition, Ubisoft may have a seventh 3DS game in the works as well. Kharijah Imad, lead designer on an unannounced 3DS project underway at Ubisoft Morocco has a LinkedIn profile that points him out as a Level Design Lead on Prince of Persia: Forgotten Sands and the level designer on Prince of Persia: The Fallen King, both on Nintendo DS.
The lead designer position on the 3DS project says "April 2010 — Present." April was before E3, so the project obviously hadn’t been announced at that point. It’s possible Imad simply hasn’t updated his profile since then. However, it’s also possible that this is the company’s seventh 3DS game.
Meanwhile, another LinkedIn profile, this one belonging to Lawrence Hum, programmer at Ubisoft Montreal, says that Hum has been working on a second unannounced Nintendo 3DS game for three years. Either this is a typo or Hum is involved with a project that was originally in development for the DS Lite and was moved over to 3DS.
Ubisoft also already canceled one Nintendo 3DS game. According to this LinkedIn profile, a game designer was brainstroming and developing mini games for an unnamed 3DS Project. Development was short, it started in February and ended in March. The designer went on to develop Michael Jackson: The Experience for Nintendo DS and PSP.