Often the problem you have described is caused by a misbehaving program running unseen in the background. Here's how you can see if that is the problem, and how you can fix it if it is:
Run MSCONFIG. Go to the Services tab. Check the box which says "Hide all Microsoft services", then click Apply. Now select everything, and disable it all. Click Apply, then reboot the computer. At this point, all of the non-Microsoft services are disabled - they aren't running.
If your computer now runs faster, you will know that one (or more) of the non-Microsoft services was slowing things down. In this case, go back into MSCONFIG and re-enable one service at a time, rebooting after each re-enable, and noting what you just re-enabled. If things slow down again, you have found the culprit. You can re-disable it with MSCONFIG, unless it is an essential program, such as your anti-virus. In that case, you should either leave it enabled, or get a different anti-virus program. Be sure to re-enable all services, one at a time, to see if there are any other problematic services.
If your computer does not now run faster, then go back into MSCONFIG and re-enable all of the services.