Here is a quick tip for you, especially if you find yourself with a clogged up machine that has trouble running even the basic programs. When you run any of your anti-spyware scans make sure that other programs are not open. Other programs being any that connect to the Internet, as Windows will see them as “in use”, and therefore they will not get scanned as thoroughly. The idea is that spyware might have integrated itself so thoroughly within the program that it cannot get removed during a scan, again cause of the “in use” flag Windows sets.
Generally when I run my scans I try and have it be the only program that is running, and run them as a scheduled task late at night, so it does not get in the way of me needing to use my computer. You can write a small batch script that will automatically reboot your machine at a specific time, and just have that anti-spyware scan be the first thing that runs after the computer has been shutdown.