Gruber points to this post by Rosyna at Unsanity regarding a bug in Apple's Software Updater. According to Rosyna, "when you see the 'Optimizing System Performance' phase of a software update, Mac OS X is really updating prebinding. Updating prebinding has a very, very nasty bug in it... If multiple processes are updating prebinding at the same time, then it is possible for a system file to be completely zero'd out. Basically, all data in the file is deleted and it is replaced with nothing." Yikes! Rosyna claims most of the problems that arise from software updates are manifestations of this bug. The upshot: "When 'Optimize System Performance' appears during the update process do not touch your computer and definitely do not launch any applications." I know some are inclined to blame the Unsanity APEs for pretty much any and everything, but I think it's worth considering what Rosyna has to say.
In response to this Gruber points to a old post of his own on updating (we even mentioned it back in the day). Basically, Gruber advises waiting a full day until after the update is released, then installing the update clean (with no other applications running), letting it finish, and then rebooting. These seem like prudent steps, and probably worth the hassle in order to avoid the prebinding bug.