My personal preference, and what I'm writing on right now, is Unity.
I am also very fond of the ROX Desktop.
What would I really like to see? Well, barring attempts to just rip up everything and start again for no good reason, I think there would be a lot of mileage in recreating some of the classic UIs of the past that many people have loved.
* Classic MacOS was a sublime UI, with a lot of subtle non-obvious features. In its way it was far more polished than Mac OS X, even now.
* OS/2 2.x's Workplace Shell was not one of my personal favourites, but it had some excellent design features, and was loved by many.
* I have an Amiga but I never was a big fan back in the day, but a good solid modern Amiga Workbench clone would have some mileage, and as I said in the article, there are already FOSS implementations, just not for xNix.
* GEM is FOSS now. Why not recreate DR's multitasking GEM/X on Linux, or any of the late-era multitasking GEM desktops from the Atari ST, such as Thing or TeraDesk?
One of my favourite UIs is undergoing a pretty good re-implementation effort, in the form of NeXTspace:
