I use a 3D Linux desktop to do my work in. I have a dual monitor setup at work and a nice high-resolution single monitor (shown) at home. The 3D desktop doesn't just give my work a nice sheen of eye-candy it also gives me valuable feedback on the health and status of my OS.
For one thing a busy application gets dimmer and gray in my desktop. So if my browser is busy it doesn't just stop responding to my clicks, I'll know its working hard well before that... I'll see it dim and go gray. If something really bad happens it will burst into flames. A moving application wobbles as it refreshes itself making the move feel substantial.
The 3D cube is a more natural way to deal with multiple desktops. I've been using 4 desktops in KDE for about a decade. But, it was easy to get lost on the desktops since they had no real spatial relationship to each other. This same feature has been ported to Windows and OSX so I'm sure many people are now enjoying multiple desktops. As far as I know these are UI changes that appeared on Linux first.
If you haven't seen Beryl yet you should. I think Beryl and Compiz could revitalize Linux on the desktop.