It may be the indexing service, but it usually doesn't run that long. If you are using win 7, run the resource monitor. Check the CPU tab to find out which process is hogging up CPU cycles. Also check the disk tab and see which files are being read/written. Have you tried cold booting the computer?
Do you have superfetch on? If so it might be possible that feature is running erratically and thrashing your HDD. If you open up your services.msc in your run command - it should be listed as "Superfetch". If it's on - try disabling it. Some people have reported better performance with it off anyway.