Sorry if I try to impart some humor here but without a few details I can't get a solid direction at times so I try the usual, the common issues I see today.
The fan slowing is quite normal after about a year so so know to swap that when we replace the heatsink compound which we do for a few reasons. Not only to be sure there are no voids but that it is not dried out and the heat sinks are mounted at all points. I've lost count of the number of times I find the heatsink hanging on by 3 out of 4 points or less.
After this we may check to see if the PSU is sized for the long haul. Again where we find a 400 Watt PSU because that's all the system needed. Think of your car at 120 MPH which it might do but for how long?
Finally we have the pests. I don't have a reason yet to move to software issues but if the machine is stable enough you can take Grif's advice for scans at http://forums.cnet.com/7726-6132_102-5098912.html?tag=posts;msg5099421