I have a Power Mac G4 800 MHz stock (no strange upgrades, standard processor, video card, hard drive, etc.) and I'm running OS X 10.4.8 and whenever I open System Preferences, no matter if I just sit there or open ANY of the settings after 5 seconds it will freeze for a good 30 seconds (some times the whole system too) and then it goes back to normal.
I thought it was something I may have installed so last night I reformatted and it does the same thing (tried it with the 10.4.6 which is what was on the DVD and then when I upgraded to 10.4.8)