What pop-up blocker are you using? The only one I like is the one with the Google Toolbar...though the one that is built into IE after you install Windows XP Service Pack 2 is pretty good.
At this point, I use Mozilla for the most part anyway, and don't have pop-up problems.
Stupid question...but are Ad-aware and Spy-bot completely up to date?
And is there a pattern to the pop-ups, or are they just random things? If they're all for something particular, you might be able to do a Google search and find what's causing them.
I'm using the IE Pop-up blocker and I've got the Service 2 pack. Mozilla really slowed things down for me.
I'm not sure about Spy-bot, I haven't updated it. But with Ad-aware I will periodically remove it and re-download it. First time I did that I went from finding 20 problems to finding over 1,000 the first time I re-ran it.