Agreed - that is one of many reason that I go back to IE regularly. Usually, I'll open both browsers, depending on what I'm doing/working on at the time.
I have the pop-up's disabled in my mozilla 1.0rc3, and pop-ups do work on most sites that use them in a legit manner. I think what mozilla is doing is blocking pop-up's that are not from the same host as the one you are currently viewing.
So say for example, here on FR.com, if a pop-up tried to open an X10 banner from another host, it would fail. If FR.com opened a pop-up from FR.com it would display.
I don't know this for a fact, those are just my observations.
The odd time I run into a site this doesn't work it, and then I just disable the setting and reload the page and it's fine, and when I'm done I re-enable it.
I haven't gotten any annoying ad banners since I turned it on, and I've been happy with it.