I'm a huge fan of the Google Toolbar in general, and the 2.0 version blocks popup ads beautifully. Unlike many of the free blockers (like Popup Stopper Free Version, which works fine), Google Toolbar 2.0 Beta allows you to click a button at any site where you actually want popups.
In my case I am on a couple of boards where personal IM-like messages are often sent to me and I had to remember to turn off Popup Stopper when I went to those sites. With Google Toolbar 2.0 Beta I have already told it that popups from those sites are fine, and poof, no popups blocked while I'm there.
Besides which Google Toolbar rocks in a dozen other ways.