This thread inspired me to run Permission Repair after performing the OS X 10.5.8 update on the computers around here. My observations were:
  • The list of "repaired" permissions on three different Macs was identical with only three or four exceptions.
  • Running Permission Repair a second time on the same Mac produced the same list of "repairs" with the exception that the three or four exceptions disappeared from the list
  • For some reason I cannot explain at this point Permission Repair on machine with by far the fewest installed applications, a MacBook Air, took almost two hours to complete the first attempt. The time for the second run on the same machine was comparable to the other two Macs.
It is doubtful it would have ever occurred to me to run Permission Repair if I hadn't been prompted by this thread.

If we knew what it was we were doing, it wouldn't be called research, would it?

— Albert Einstein