I actually do run ion3. The only problem I've had so far is that some of the Alt+ keyboard shortcuts interfere with some Emacs shortcuts. One off the top of my head: Alt+G.
I just remap/unmap the ion shortcuts to get out of the way of emacs. I have a friend who swears by setting ion's Mod1 to capslock, but my pinky just can't handle that.
OK, not really my desktop. But ion is quite cool.
About 50% of my programming time is spent staring at a maximized vim instance, and about 30% staring at a maximized firefox instance: http://jey.kottalam.net/tmp/screenshot.png