Just in case you were unclear on the issue, both Reggie Fils-Aime and Satoru Iwata have clarified the role that 3D will play in the Wii U. So, as explained by Reggie:
3D gaming without glasses is a key part of the proposition. There may come a time when 3D without glasses becomes appropriate for console, but we don’t see that in the near future.
In a separate instance Iwata expanded on this, saying that:
If you are going to connect Wii U with a home TV capable of displaying 3-D images, technologically, yes, it is going to be possible, but that’s not the area we are focusing on.
He also notes that “rather than pouring a lot of energy into that kind of area, with the Wii U we’d like to focus more on each Wii U owner being able to have an equal opportunity to enjoy it.”
None of this is too surprising, but 3D is technically possible in the sense that if you hook it up to a 3D-enabled television and a developer has designed a game with 3D in mind, then it’ll work as intended. Just don’t expect any attention from Nintendo.