Daniel-
The "Nu" in Nupedia means next to nothing other than to be phonetically similar to "New." A new encyclopedia. So what? GNU, however, means free as in content freedom.
It also means GNU, that is, the GNU project (www.gnu.org). And that brings with it a whole baggage of other connotations. Nupedia is bland. That can be a good thing sometimes.
Regards,
Erik