Is it safe to install Windows Updates on a Boot Camp'ed OS? I just installed Windows 7 on Boot Camp, and when I login to windows, it says that there are Windows Updates available. The problem is that one time when I tried to install these updates, it prevented Windows from starting up again. So I'm wondering if it's okay to run all of the Windows updates as they appear, if I have to avoid some of them, or if I have to wait until Apple releases a patch which would permit the updates to be installed without any adverse effects.

Here is the series of events that occurred as I remember them:


Installed boot camp
Installed Apple's drivers via a USB flash drive
Restarted
Connected to internet
Windows noticed that there were a few recommended updates and installed them.
Restarted
I manually checked for updates in Windows Update to see if there were any more, it showed 40 or so.
I began the update process.
While it was downloading and installing the updates, I ran Apple's Software Update. It showed that there was an update to Boot Camp (3.2, I believe). I didn't install it since Windows Updates was already in the process of installing updates.
Restarted
Windows didn't load, instead Startup Repair loaded which said that Windows was unable to load normally.
One of its suggestions was to perform a system restore, I approved this.
After some time, Startup Repair said that wasn't successful at finding a solution. (It's ambiguous as to whether or not the restore worked.)
Restarted
This time it launched Windows correctly.
I checked how many updates there were in Windows Updates, and it showed only 4.
I launched Apple's Software Update, and updated to the latest Boot Camp.
Restarted
This time when I checked for Windows Updates, it showed more than 40.


My guess is that the restore did work, since after restarting, Windows launched. Plus, it showed more than 40 updates left.
For practical purposes, when you boot into your Boot Camp partition you are on a regular PC: All updates pushed thru Windows Update should work as expected. I have used Boot Camp since the beta period all the way to Snow Leopard and I have never experienced a situation like the one you describe. 

I believe that Windows Update will only push updates that are critical (like security updates) and everything else (like driver updates) is listed as optional. I recommend enabling the option that makes Windows Update prompt you whether or not it should install updates when available. That way if you are in doubt, you can always review and make sure any driver updates are not pushed into your system, and things like security updates are. 

It might be a good idea to stick to the drivers provided by Apple. 

I am unsure why you had to manually install the drivers on a USB drive, since they are usually installed automatically from the Mac OS X DVD right after Windows completes its setup. I wonder if there is a particular situation with your system and that the fact you had to install the drivers separately is related to what is causing your hardware to be unreponsive now.