CodingForums.com - Firefox 1.0 Tips and Tricks has some good tips on optimising and stopping some new popups.
The only thing that I would change on the user.js file is set the privacy popups to 1 instead of 2 (so they are treated the same way normal popups are) and also add the line
user_pref("dom.disable_window_move_resize",true);
to the file - this stops windows from being resized.
I've not actually come across any flash based pop windows yet so I'm not really sure if I'd want it set to 1 or 2 but as 2 denies all popups, there might be a case where I want a popup to occur and this would block it.
There's quite a few like that on snopes.com, unfortunately.