This tip’s headline is a bit alarmist — so let us clarify. When you are running software updates, or installing new security patches, you shouldn’t do anything with your Mac while it’s running through the last “Optimizing System Performance” phase of a software update.
Launching applications while your Mac is performing this last phase of a software update can potentially damage system library files. In the worst case, there is a chance your Mac won’t be able to start up again without significant troubleshooting.
Note: We can’t vouch for all the technical details behind this supposed bug, but you can read about it at the Unsanity blog.
We recommend you run security updates at the end of the day. Ideally after restarting and with no other software running at the time. While Apple’s software update feature does not make it easy to tell when a particular update was released, we generally recommend waiting about a week after a major update is released before you install on your Mac.
For our clients who schedule regular monthly maintenance visits, we generally run all software updates on each Mac once a month after a fresh reboot.
Source: This tip inspired in part by a unbootable MacBook Pro at The Matale Line which exhibited symptoms of this bug after an iTunes upgrade on a busy multitasking laptop. Additional details on TUAW, with general advice on software updates on John Gruber’s Daring Fireball.