Ive recently discovered that a harddrive that checks ok with scandisk, or chkdsk is not necessarily a good drive.
I have run the new HDTUNE program on systems that seem to have too much HDD activity but check out ok, and found that there are many many slow sectors. HDTUNE has a SPEEDMAP option when you check for errors with the QUICK box unchecked.
The speedmap shows sectors that check error free, but are slower than other sectors, basically making the harddrive re-read that sector repeatedly...
In some cases reformatting the drive in either low level or standard (not quick format) repairs the problem.
The test on my old drives went from @40MB/s to 80+ MB/s average, these are SATA2 drives that are about 5 years old or older.
On the old drives that could not be improved, were cloned to a new drive and the system performance is night and day!
The speedmap is an invaluable tool for diagnosing excessive harddrive activity when all spyware, and viruses are known to be already removed in a system that is very slow..