I have an idea and I believe that this new breed of popups is primarily caused by Macromedia Flash.
Firefox is set to block popups caused by the standard code that makes up web pages. Flash however is a plugin with rights to open popups on its own. Unfortunately, if you block it's ability to do so, you may hinder safe Flash content from performing as designed.
My solution is to use the FlashBlock extension for Firefox (
http://flashblock.mozdev.org/). FlashBlock replaces Flash content with a placeholder on the page that allows you to click to view the content. It has a whitelist so you can turn on Flash (for every visit) on pages you trust.
I have used this extension for some time now simply because advertisements were becoming too distracting - hindering my reading. I noticed that popups began appearing on one of my computers that did not have Flashblock installed while I saw no new popups on those with it.
I hope this helps.