In the past I did a lot of dloading/uploading and file transfering over a long period of time and I realized that my comptuer ran slower after that, it didn't seem to be my CPU/Chipset's problem because their temperatures were normal. I felt the HD and it seemed pretty hot, or at least hotter than when it is at idle, so after I let it idle for a while, I felt that hte computer ran much faster.
I built a little CPU Fan/HD cooler myself using cable ties. You'd be surprised how cool that little fan can keep your HD.
G. Skill 4GB(2x2GB) DDR800
eVGA 8800GTS 320MB
super pi: 1m=20s