Last Friday I came upon a frustrating problem with a Windows Vista system that had applied updates during shutdown, but could not finish the process. This resulted in many reboots and an unusable computer; too bad it held the company's only copy of QuickBooks.
Typically the simplest fix is to boot from the Vista install media and choose Repair, then System Restore. The trouble with this system was that System Restore was turned off and there weren't any checkpoints to go back to.
Enter the endless search online. More IT troubleshooting by Bing and Google. I'm not exactly sure which search engine got me there, but one forum listed the answer (albeit two hundered or so, lines down the page).
Boot from a Vista or Windows 7 disk and choose Repair, then Recovery Console. Once you have a command line to work with, cd to C:\windows\winsxs and del pending.xml, exit to reboot again and you'll see the "Configuring Updates..." message once more, but it will continue to the Windows login screen allowing for celebrations all around.
This was the fix that worked for me, hopefully you'll have the same luck.