In his weblog, Robert Scoble talks about whether Microsoft's Longhorn should still be called Windows. He mentions a few pros and cons why it should or should not be Windows. While a new name will mark the enormous shift that the OS is undergoing, I strongly think that it will be labeled Windows for years to come.
Think of brand recognition. Sure, you don't want people being confused about whether a piece of software will run on it or not. Scoble mentions that apps designed for Longhorn will not run on Windows XP, well, a lot of XP apps don't run on Windows 95 and most surely not on Windows 3.11 (let's forget the versions before that one). The one common denominator: Windows...
I remember someone mentioning a review session of the .NET Framework attended by Bill Gates. At this point it was in alpha or something, but there was no namespace containing the name Windows, he ordered a change. Win.Forms should be Windows.Forms...
Anyway, marketing and nostalgia will make sure that the Windows name will be used for Microsoft's OS for quite a long time.