This may be a stupid question, but how many fonts do you have installed on your system? Excess of maybe... 8-900? I've got over 20k on mine, but NOT installed, I use a font management software for mine.
If you've got a TON of fonts installed on your system, it decreases system performance substantially. Otherwise, i would begin backing up my important documents now as someone else suggested, and running a few tests on the hdd. A few sectors may be failing at this point.