My procedure for a major OS or Security update
I never run a major update right away. I always wait at least a week or so to see what develops. Most problems I see here are the result either of a specific incompatibility with a third party application or plug-in, or some pre-existing software or hardware issue related to that unique user, which only comes to light due to the stress an update writing many thousands of new files causes. Then, there are occasionally, presumably, as in the instance of font and PDF problems with the 10.6.7 update, bugs in the update itself, which affect the majority of users.
External drives are not that expensive these days. I have two clones on externals and if I'm concerned enough about an update, I can install it on one of these and test it first.
Here's my own updating procedure. Major updates don't come along that often. It's worth going to the trouble to do this.
1. Have a backup, so if something does go wrong you won't be left in big trouble.
2. Verify and if necessary repair the drive from Disk Utility. (To repair, you must be booted from the Install Disc or an external clone.)
3. Disconnect all peripherals except the keyboard and mouse.
4. Download the Combo Update from Apple Downloads. It's generally more reliable to update from the standalone Combo than from Software Update, and the Combo, as it includes all updates from 10.6 onwards, may correct any files that have been corrupted or somehow gone missing.
5. Boot in Safe Boot. Hold the Shift key down at start up. Give it time, it will take longer. (The Safe Boot will also actually check and repair the drive if necessary--and if possible.) Safe Boot loads a stripped down system which may reduce any chance of incompatibility while the update is running. Keep all Applications closed.
6. Repair Permissions from Disk Utility while booted in Safe Boot.
7. Install the update from Safe Boot. Keep all Applications closed.
8. Restart when prompted and give the system up to five minutes to finish the final touches of the update with all Applications closed.
9. Verify the Drive and Repair Permissions again.
10. And then I like to restart again.
One other caution. If you are running updates from Software Update, run them one at a time, never all at once. This gives the system a chance to assimilate each one, especially if restarts are involved, and not choke on them.
I also prefer to get "non-major" updates as standalones from Apple Downloads, rather than from Software Update. I only use Software Update to see what's available.
NEVER INTERRUPT AN UPDATE IN PROGRESS EVEN THOUGH IT APPEARS TO BE STALLED