Try force quitting System Preferences.
To force quit an application, choose Force Quit from the Apple menu (or press Command-Option-Esc), then choose the unresponsive application in the Force Quit window, and click Force Quit.
Optionally, you may be able to Option-right click the application's icon in the Dock and choose Force Quit from the contextual menu.
Additionally, you can force quit the front-most application in Mac OS X v10.5 or later by pressing Command-Option-Shift-Esc for three seconds.
I recently started experiencing the exact same problem. This started randomly, just one day I tried changing my desktop background, and the whole desktop and screen saver window started not responding. Then I force quit the application, and tried opening the system preferences through the apple icon on the top left, which is when i realized that this is pretty serious, considering i cant access anything in the system preferences menu.
I have the new Retina Display Mac Book, with Mac OS X 10.7.5.
I havent done anything to fix the problem, but im growing desperate.
Also, I have tried rebooting the computer, does not help.