BumpTop is a pretty slick way to look at a user's desktop. Having a 2D desktop is pretty played out in Windows. Nothing all that cool has happened since Windows 3.2, and I don't think Vista will offer a whole hell of a lot. While Apple has done some nice things with the floaty taskbar thing, or dock, or whatever it's called, it's still in the X-Y plane. I'm sure there are other 3D desktop mods out there, but I haven't sat through any of their 7 minute vidoes like I did with BumpTop.
However, I don't know how much organization a user really does on the desktop. Regardless, it's pretty and probably fun for a while. How long till someone does something like this in Flash for the web? Maybe it's already been done? Maybe I need to look around some. Maybe I already did... though it's not a web/flash doodad, here's another 3D desktop: Kororaa and here's a video of it in action.