… as in going from 10.9.4 to 10.5, or from Mavericks to Yosemite.

Step zero:

0) if you do not have MenuMeters AND are showing its disk lights, now would be a good time. ( http://www.ragingmenace.com/software/menumeters/index.html )  Free.

(MenuMeters will show you when your drives are active – being read or written. This is “a good thing” and useful if you plan to follow the optional steps below… so get it and install it now.)

then…

1) visit http://support.apple.com/downloads/ and find the updater that has “combo” in its name. Download that.

2) Repair Permissions

3) if you have not run DiskWarrior in a while, now would be a good time. (http://www.alsoft.com/diskwarrior/ )

4) reboot

5) quit any running programs and double-click the installer.dmg you downloaded in step 1).

6) run the updater. (This will require a reboot.)

7) once the desktop appears, don’t do anything until the menu meters disk lites are quiet (black).

Now, here is an optional massive Roto-Rooter of your system:

8) run Mavericks Cache Cleaner and do a full system maximum cleaning.  ( http://www.northernsoftworks.com/maverickscachecleaner.html ) This step may be skipped.

9) do a safe reboot:

To Safe Boot, follow these steps.     a. Be sure your Mac is shut down.     b. Press the power button.     c. Immediately after you hear the startup tone, hold the Shift key.      d. The Shift key should be held as soon as possible after the startup tone, but not before the tone.     e. Release the Shift key when you see the gray Apple logo and the progress indicator (looks like a spinning gear).

10) wait for the desktop and then wait for the menu meters disk lites to be quiet (black).

11) reboot

12) and again wait for the menu meters disk lites to be quiet (black) before starting to use your shiny scrubbed Mac with its new OS.

(Some folks will say to rebuild permissions here. Well, it won’t hurt, but likely isn’t really necessary.)

As usual, this is just my opinion, and how I do my own machines, and those of my clients. It’s been a good routine for me, but I cannot take responsibility for what you do, even if you follow these steps exactly. There are just too many variables involved, so you’re on your own. If your Mac suddenly refuses to grill a proper hot-dog, it’s not my fault…