Seems a common problem. How to fix?

Pop-ups are usually advertisements put in place to load with the site you are visiting.

Try this: http://adblockplus.org/en/ and this: http://www.mywot.com/ Former blocks the ads from ever appearing; the latter rates safety of the ads that do show.

Clarification request here: Ads displaying are a part of the website, and not a true pop-up in the sense that you have a separate window for that ad? Example: Ad on top of the site that pops up in the center of window you are visiting; it follows the scrolled window only to remain centered in the display at all times? AdBlock Plus will take care of that. A good example of a really obnoxious advert that will not be ignored. Gone with AdBlock.

Be sure to donate to them; add-on is free to use otherwise and is customizable.

Vendor will work with users to continually update against unwanted and malicious and aggressive advertisements; users send in info for them to update.