I use Software Update, and haven't had any issues with an update for a long time, but this one threw me a curved ball. I noticed that my Dock CPU utilisation was 90%-ish - that's a whole core out of my four. This was impacting the CPU available for Folding@Home, plus it affected system responses generally. I tried shutting down apps, rebooting and so on, then checked out the interwebs and found this:
http://reviews.cnet.com/8301-13727_7-20074173-263/do...
I applied the work-round in the above link (turned off WIndows app icons in the dock) and the problem went away. Even when Parallels wasn't running, it seems it had a daemon polling for Windows application icons to show in the dock.
I doubt if my use of Software Update had any effect, as this looks like a Parallels issue.