My pointers for OS system upgrades. These should be fairly obvious and logical, but surprisingly I see and hear of people who will try to run an upgrade, with 5 apps running, downloading files, and so on, then wonder/complain that the upgrade 'screwed up' my system.
1. Perform Verify Disk AND Repair Permissions BEFORE upgrade.
2. Boot from another partition or drive, other than the one being upgraded. This ensure the partition to be updated is completely accessible and no files are open or in use. In this day and age of inexpensive supersize hard drives, there's no reason not to have an extra partition to boot from for situations like this. It doesn't take much space. A bare bones install of Mountain Lion will fit on a 10 GB partition. What's 10GB on a 500 GB or 1 TB drive? Disconnect all other external drives/unmount other partitions, other than one you booted from and the one to be updated.
3. If unable to boot from another partition or drive (i.e. you are updating the same installation you booted from), then before starting the installation, shut down all apps, including any of the apps that run on the menu bar if you can. (us old Windows people will remember the old saying about quitting all TSR - Terminate and Stay Resident- programs before doing any Windows updates, this is kind of the same thing, turn off all those third party apps running in the background). Go have some coffee while the upgrade is in progress, really you don't need to be working at the same time, those 15 minutes are small compared to the time you will waste if the install goes bad.
4. Perform Verify Disk AND Repair Permissions AGAIN AFTER the upgrade finishes and the system reboots.
5. I run the Combo updater, even if I'm just upgrading from one point release to another. For newbies, Apple releases OS updates in two forms, 1) a smaller update that updates from the immediate prior release, like if you have 10.8.4 installed and want to upgrade to 10.8.5, and 2) a combo updater that updates any prior version. For example the 10.8.5 combo updater will update any version from 10.8.0, .1 , .2, .3 and .4. Why run the combo, even if just upgrading from the previous point release? There have been times when Apple has forgotten files in the point upgrade, and the point upgrade is based on just covering the delta between the two points releases. The combo makes no such assumptions and includes all files changed since the dot zero release, and during the upgrade, a simple date/time and version check tells the updater whether to copy over or not.
When you consider that OS X has HUNDREDS of THOUSANDS of files, the possibility of human error in packaging when applying cumulative point release updates on top of each other is likely higher, versus a combo which makes no assumptions about what got changed in between. I do not have any proof of that, this is a personal opinion, I could be wrong, but in my experience I have had good results always using the combo. Besides if you read any of the Mac publications and tech pundits, nearly all of them recommend using the combo as well.
If you have multiple Macs, or work in a multi Mac shop, it's also a lot simpler to keep one combo updater on hand, than multiple point updaters.
Hopefully, if you follow these steps it will minimize the possibility of those spurious, hard to pin down, system hick ups that are often reported here.
Lastly, laptop users with smaller drives that feel they can't afford to set aside 10 GB for a boot partition, invest in an external drive, it's well worth it. If you have a Time Machine drive, you can even partition off 10GB on that.