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What version of Mac OS are you using ? I have had similar problems which I may have solved buts its still to early to be sure as I only implemented my solution yesterday.
My problems started when I upgraded from Snow Leopard to Lion and my whole system became unreliable with frequent beach ball and random freezes. I tracked the fault to an old snow leopard driver for my Wacom Bamboo graphics tablet. My system now feels like a new computer since I upgraded the driver to the latest/Last Lion version. While you may not use a Wacom you may have other legacy drivers that might be causing your system problems.

best wishes