Go to your add/remove programs and look for some things that were installed you don't recognize and uninstall it. Some websites install pop up or tracker programs on your computer.
1. Spybot doesnt block popups (not enough to be considered a full popup blocker)
2. If you have the patience for it, grab a good firewall like Kerio or Sygate and nail the individual IPs (i.e., blacklisting) for all the popups or better yet, do everything via whitelisting (there are also automated antipopup features in there too)