And I call BS on your statement. Yes, permissions are a crucial part of any UNIX based system. But you do NOT find a "repair permissions" application or tool in any other UNIX based OS than Mac OSX. Ive used GNU/Linux since 1997, and I have never even heard of this "problem" before buying a Mac.
A permission problem is really simple: Either you have the permission to do something, or you dont. Every mac user constantly claim repair permissions when you see some erratic behaviour on a Mac system. I dont buy it. In fact, you would have to boot of a Mac OSX install DVD and launch disk utility from it, in order to repair your boot volume. Reason: It has to be unmounted before repair permissions work.
Just try for yourself after the 10.4.3 update. Click repair permissions 100x for all I care. You will end up with the exact same files with wrong permissions afterwards. However, booting of the install DVD and doing the same thing will correct the problem - until you boot from HDD again, and the permissions have been screwed up yet again. Prove me wrong