Is it a virus or spyware?
If it's a virus run any software you have or try a PCCillin online scan. Personally, I find anti-virus software doesn't actually stop much from getting on your system but what it does do is let you know which virus you are dealing with. Once I get the name of the virus I usually head over to Symantec's site to see if they have a virus removal tool for the virus in question. They are usually small executable files that take care of the work for you but you have to follow a few instructions which are pretty easy. If you're lucky you'll find a tool on the site but if not you'll have to Google the name of the virus and hope someone else has some step-by-step instructions for manually removing it.
If it's spyware try running Ad-Aware and Spybot Search & Destroy. They both seem to pick up on different objects that are running so most of the time you really need to run both. Hopefully they'll pick up a few things which you can then remove but sometimes that isn't enough and this is where knowing your MSCONFIG start up files helps. If you've remved everything and you're still getting pop-ups I usually then run MSCONFIG and go to the startup tab and start unchecking anything that looks suspecious. Reboot and see if that helps. Sometimes these programs will be loaded in folders like "Microsoft" but it will be placed somewhere weird like your My Documents folder so that should raise alarms.
Anyways, if you have any more questions let me know. I'm not the greatest at fixing these problems but I have owned a computer that had to be plugged in to a university campus network so I've done my fair share of virus removal.
Oh and GL and GG.
