Apparently those pop ups are launched by plugins - flash, for instance. There's an easy way to block them, though, and it's built right into Firefox already.
Open a new window or tab, and in the address bar, type "about:config". Just like that (minus the quotes). Hit enter.
Right-click in the window with all of the options, and go to New -> Integer.
Inside the New integer value box, type "privacy.popups.disable_from_plugins". Again, just the stuff inside the quotes, not the quotes.
Inside the resulting privacy.popups.disable_from_plugins box, type either 0, 1, 2, or 3.
0 = disabled
1 = partial (pop ups are allowed, but the number is limited)
2 = full w/ whitelists
(3 = block all, including whitelisted sites - not sure if this works, but even if it does, why would you want it...?)
I recommend 2, personally. With 2, you will still get the little bar saying "Firefox prevented this site from opening a popup window. Click here for options..." and if you want to allow that specific site to show pop ups (lets say it's part of the app/site design and not malicious), you can white-list that one site. Since turning it on, they've all gone away.
"Test" sites you can check to see if it's working:
Found here: http://weblogs.mozillazine.org/asa/arch