Some of the recent advances in GUI have been good. The OSX inspired pinning of applications to a unified taskbar where mouseovers show active instances is something I like, and it is now present in gnome3, unity, windows 7 / 8, and osx. I think you can get it in XFCE through some addons.
Another thing I like is the menu global search they are all implementing. In the same way that google is the front page to going places on the internet through search, I feel in the long run it may not be a good idea to indoctrinate people into the idea of search being how you find everything rather than by the file system, but for the average joe it is a great abstraction of the system. Makes finding stuff a breeze if you know the name.
Some other stuff, like making the GUIs take up large fractions of the screen (cough, unity) or have flashy FX (windows, osx) is all gloss with no purpose, and doesnt really belong in the GUI.
I think the problem is that GUIs need to be designed by what is natural to the user, instead they are all just trying to copy the current most popular OS even if its GUI isnt remarkable.