A little less than a year ago I talked about in my post "The Power of 3D" the future emergence of 3D in the user interfaces of standard applications, not just video games.
While we see some of this already here in the Macintosh with its three-dimensional "fast user switching" in Mac OS X and, coming in Tiger, a very unique video chat, I believe that Avalon will spearhead widespread 3D UI with its integration of 2D, 3D and Media into a single compositing pipeline.
To get an idea of the user interface possibilities, look at the Microsoft Research UI prototypes being developed for Longhorn. Another glimpse can be found in the recent demonstration of Avalon 3D in Channel 9. The current alpha of Longhorn actually sports three-dimensional task switching.
On the other hand, there's been many third party attempts to extend the shell's desktop with a 3D metaphor. Sun currently is working on a 3D desktop project called Looking Glass. I don't personally find a 3D desktop, where one has to traverse a maze to locate files or launch applications, as compelling as simply using 3D effects in the UI. Three-D effects feel much more natural and use less screen real estate.
I look forward to the day when both 3D user interfaces and new autostereo 3D displays (announced last year by Sharp) become commonplace; the combination of the two will literally be eye-boggling.