You did not include your operating system or tell us what scans you have run, so based on that, all I can do is give general information.

Please run these scans:
a. Ad-aware: http://www.lavasoft.de/software/adaware/

b. SpyBot S&D: http://safer-networking.org/en/news/2005-05-31.html

Then run an online scan here:
http://housecall.trendmicro.com/ You will need to allow Active-X (click the bar at the top of IE7.)

If your problems continue, please post a HijackThis log over on the HijackThis board. Please include info on the type of popups that you are getting. That way we will be able to diagnose your problem accurately.