Reports are coming in from all corners of people who installed Microsoft's Tuesday round of patches, rebooted their PCs, then got stuck on "Stage 3 of 3. Preparing to configure Windows. Do not turn off your computer." The afflicted computers will sit like that for hours.
The solution, predictably, is to turn off your computer. The easier approach is to use the Ctrl-Alt-Del three-finger salute, which pops you right back to the login screen. In either case, you will discover that all of the Tuesday patches have been successfully installed and seem to be working properly.
At least, that's how it looks right now.
The problem appears to happen on both Windows 7 and 8.1 PCs, both 32-bit and 64-bit, running on domains, running on Windows workgroups, and running standalone. One updater reported that the hang happened after installing KB 3020370, KB 3045645, KB 3020269, and KB 3013531, so the current best guess is that a combination including one or more of those four patches does the dirty deed. (t/h DD)
It also looks like installing the patches one-by-one doesn't trigger the problem. (t/h VG)
Initial reports blaming KB 3046002 appear to be erroneous. (t/h SB, EH)
There's an epic Reddit thread on the subject that starts with a consultant saying, "Microsoft is making me a fortune this morning."
And so it goes.