Im my opinion I would switch to using mozilla or firefox browsers. THey are much easier, faster and have more functions than IE can begin to offer. They also come with a popup filter that allows you to not accept popups. If you like to look at multiple pages at once they also offer tabbed browsing which is an excellant feature and both browsers are free to download.
If you are hung up on IE and you are getting the popups there could be multiple reasons. Certain sites you visit may pay for there web hosting by the little popup advertisements in hopes that you would click on them. You could always install a popup blocker so you will not get the advertisements.
If you have just started getting the popups or they have recently just became a big problem maybe it would not hurt to get hijackthis and run it to see if you may have gotten something and that's why you are getting the popups. Whetherr my advice is the greatest that is what I would do if I were you...best of luck to you.