Loads of things it could be, I would suggest you search the forum under "slow PC" of similar, it's a mine of information! One thing many people do not check though is to take the side off the PC and have a look at the heatsink on the processor to see if it is chocked up with dust.. This is often the culprit if everything else seems to be in order, the processor gets too hot and slows down.
If this is the case with a small artists paint brush and careful use of the hoover it can easily be solved, you may have to take off the fan if it is really bad.
Other than that apart from a virus scan, run spybot S&D and AdAware. Do a system file check to see if any of the windows files are missing or corrupt. Go to start-run and type sfc /scannow and have your operating disc ready.