Here is just a list of the steps I use to clean out basic infections. For the harder stuff you'll have to do some extra stuff.

• First thing to do is test the harddrive to make sure it is not failing, what's the point in cleaning out infections if your drive is failing. I usually use IBM's Drive Fitness Test. www.tacktech.com has all the latest diagnostic programs for all brands of harddrives, the IBM one is included also.
• Next If you are running Windows Vista,Windows XP, or Windows Me, you want to turn off System Restore (click the link for instructions). If your system is infected and system restore is on, then there is a good chance that the infection got backed up.
• Next would be to clean out any temp folders, temporary internet files, and running Disk Cleanup. Infections love to hide in temp folders.
• Next install and update anti-spyware and anti-virus programs. The programs I use are; Ad-AwareSE, Spybot S&D, SpywareBlaster, HijackThis, and AVG Free anti-virus. You can use whatever you want, but these are Free and work great!
• Now I usually like to do my first run in SafeMode. Once in SafeMode run Ad-AwareSE, then Spybot S&D, then AVG Free anti-virus, lastly HijackThis. Now, HijackThis can be a tricky and confusing program to use if you never used it. The best thing to do would be to save the log file and post it on a spyware and virus removal forum. Tech Support Forums is a good place to start. For me, I am used to using HijackThis, so what I do is look over the log and write down anything that doesn't look right, then I google-it.
• Once all that is done reboot into Normal Mode. Here I usually do one more scan with all the tools, just to be safe.
• Next run Windows Updates.
• Next run Disk Defrag.
• Don't forget to turn System Restore Back on, and your done.