There’s a lot that a 3D desktop can do that it shouldn’t - just look at some aspects of Vista’s desktop
But things like the pager & task list showing perfect miniature views of the actual window, true transparency, accurate drop shadows et al would be a very useful addition to any desktop.
Maybe the next major release of FVWM would be FVWM3D?
Mind you, I think that just making 2D windows look a bit more 3D isn’t making the best use of the possibilities - I reckon the future interface won’t have windows at all, all the individual items that live in individual windows will be freely moveable between apps.
e.g. when you have an IM conversation with a friend in another country who’s got a blog, you’ll have an IM text box, plus the blog’s RSS feed, a clock showing what time it is for him, and maybe his current weather as well, all in one place instead of in multiple independant windows.
But that’s just an opinion, of course