Seriously, there are many Win apps that violate the standard Win rules (viruses, trojans, and poorly written popular apps). I have come across many situations where an unruly app refused to pass system control to the shutdown script, and the system just seemed to hang forever.
If that is the case, killing or removing the offending app will cure the problem until you run the app again. Also, I have seen more than a few cases where the Win memory manager simply eats itself, and dies. That was pretty much the signature suicide of Win ME, and has been mostly fixed since then, but it still rears it's ugly head from time to time with more modern Win OS's.
If that is the case, even the keyboard will freeze (num and caps lock buttons will not change state), and there is little to do but pull the plug on the PC. I know that pulling the plug is taboo, but hey, if you run a Windows OS for a long enough time, you WILL know where the power button is located on your PC.
Voyager