The Xenoblade developers get a special thanks from the Zelda team.
http://www.nintendoworldreport.com/news/28377
Monolith Soft, the Nintendo-owned studio responsible for Xenoblade Chronicles, is listed in the credits of The Legend of Zelda: Skyward Sword.
The nature of Monolith Soft's involvement is unknown, but it is likely they consulted on Nintendo's latest epic in some fashion.
Additionally, Nintendo-owned developer Brownie Brown was listed in the Super Mario 3D Land credits. Like Monolith Soft, their involvement in the game isn't precisely known.
Nintendo gained controlling interest in Monolith Soft from Namco Bandai in 2007, around the time Disaster: Day of Crisis was being made and released. Since then, they have made Xenoblade Chronicles, and are rumored to be working on a Wii U title according to job postings in June 2011.
Brownie Brown, developers of Mother 3 and the Professor Layton bonus game London Life, was founded with funding from Nintendo in 2000.