Have you tried closing down all other applications, including anti virus applications (you may remove internet connexion while doing it)?
Yep. Shut down everything, including all fonts.
My system is loaded (Dual 1.8 GHz G5, 1.25 GB of memory).
Uhm.. that's "loaded"? That's like the slowest G5 made with almost the minimum amount of RAM.
But.. I agree with you. Clipping masks seems to drastically slow CS4 down. Even if an object isn't really complex, but included many objects. I'm running a much faster system than you are and I have to wait around 3 to 10 seconds after any operation for some files. It's annoying. So far, I've not found any solution other than to expand and clip the masks.