Repair Disk / Repair Permissions -- which first

Question

If I want to run repair permissions or repair disk, which should I do first?
Does it matter?

Answer 1

"Repair disk" makes modifications to the structure of data on the disk itself. If there is an error, this really needs to be done first since the errors could manifest themselves as botched permissions, mangled files, etc. If the disk's integrity is actually compromised, the highest priority is to repair it. One thing to keep in mind is that certain repairs cannot be made on a mounted disk (such as the one you boot from), so for the disk repair procedure to work, you should boot of another disk (your OS installation disk, a bootable external hard disk, etc.). Even then, Apple's disk repair is curiously basic -- there's many errors it simply does not detect or fix and for that you need something like DiskWarrior. Mind you, disk errors like that shouldn't occur, and if they do you may have hardware issues to be concerned about.
"Repair permissions" compares file ownership and permissions in a directory to a list stored in the package bundles in /Library/Receipts. If there's a difference between what it finds in the file list stored in the receipt package, and the files on disk, it attempts to set the permissions and ownership of the file to what appears in the list (which should reflect the state of the file when installed). It doesn't do anything at all to preferences, user preferences, user files, logs, file created after and application is installed, etc.
Contrary to popular belief, repairing permissions doesn't generally do much for you. It should be pretty rare that it finds a difference unless you've really been mucking about, and generally when it does find something it's either because you explicitly changed the permissions or because there's some other problem where an application or disk issue is changing the permissions. The one time where it really makes sense, actually, is after you repair a disk issue.
It's common advice that people tell you to repair permissions as a step to address problems, but mostly because it's an easy thing to do. Similarly, zapping your PRAM is frequently advised when trouble-shooting, though the process of a cold-boot (complete power-off, then power back on a few seconds later) is generally the portion of that procedure that actually produces the desired result.