About the repair permissions thing... If you have a Mac OS X Panther 10.3.x Mac, this is very true. But if you run Tiger 10.4.x, the repair permissions thing has been fixed.
As for freebie maintenance utility apps, you can check out
OnyX: it's very powerful and it does plenty of things.
Another one that I love and use on a daily basis is
MainMenu. It does some of the same things OnyX does.
One thing I would recommend you buy and keep in case of big emergencies is Alsoft's
DiskWarrior. This app has saved my hide when I thought nothing would. Like for instance a recalcitrant iMac after a power failure while I was using it. I kept getting the grey screen with the spinning disk and nothing would come on after that. DiskWarrior fixed everything in the directory. :girl: