Another way to test whether a browser extension or toolbar is causing the popup ads is by using IE's InPrivate Browsing function.
In IE, click Tools > InPrivate Browsing or use the shortcut CTRL+SHFT+P, and try going to the same sites you normally visit. InPrivate Browsing disables extensions and toolbars. Are you seeing any popup ads? If not, then its likely being caused by an extension/toolbar. If still seeing the ads, then may be the result of an installed program. In which case, go to add/remove programs and look for any suspicious or unknown programs.