The IDE bus that the hard drive is plugged into by default can get "worn out" on a computer that is in use a lot of the time (work horse). I don't know if it's something to do with solder or what. The fix is to put your hard drive on the other IDE bus (the one the optical drive plugs into). You will have to do a master/slave setup to use both drives. I've also found that it can be very convenient, but a little tricky, to put the hard drive into the zip drive bay (if it's empty of course).
I've seen this hardware problem on three computers in the last three years -- a Blue & White G3, Graphite G4, & just recently on a QuickSilver G4. So I can't even imagine how many towers are out there with this issue. I have one of these "fixed" G3 Blue & White towers in my home today, and it has worked just fine for two years after this fix.
[robg adds: I obviously can't test or confirm this one through personal experience, but I thought it was intriguing enough to post as a possible solution for what might at first seem to be OS X issues.]

