File permissions have nothing to do with it (the advice to repair file permissions seems to be the Mac equivalent of "defrag disk, run anti-virus scan" in windows).
Ever since upgrading to Leopard, I have experienced intermittent system freeze-ups on my Mac Pro (I never had a single one under Tiger). These happen usually while running an iTunes visualizer, screen saver, or playing a dvd. This implicates either the graphics hardware (I have the ATI X1900XT) upon which Leopard makes more demands or the (ATI) graphics drivers in Leopard.
Freeze-ups are a known problem in the new iMacs with ATI cards. Most Mac Pro owners I've heard from who have experienced this also are running the X1900.