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:
http://birthday.yahoo.com/netrospective/ <-- this is a case of a site where the app won't work until whitelisted - but whitelisting it just requires clicking on the "Click here for options..." bar and clicking to allow it. To see this in action, click on any of the pics, and then click a red-underlined link. It should bring up a new browser window, but Firefox will block it if you've set the disable_from_plugins option to 2.
Found here: http://weblogs.mozillazine.org/asa/archives/007682.html