There are several good reasons that popups have been addressed and consigned to the developer's version of termination. First and foremost, it was one of the biggest requests by users for IE.
But, there's another great reason for putting popups in our sights. Non-user initiated popups take control away from the browser user. That can cause anything from annoyed users to panicky users who do the wrong things in reaction to the unwanted popups. It gets potentially worse... either a hapless user gets shunted over to a socially engineered black-hat hacker website and provides information s/he should definitely NOT... or our hero downloads a piece of nasty malware inadvertently.
In strides SP2, and the completely reworked Internet Explorer. Now the popups are recognized, tagged and blocked by IE early on. No more full-screen popups that are impossible to remove. No more annoying popups which are offscreen. You get the picture.
But this leads me to the next part... DHTML. If you think that the popup writers are just going to give up and become good website citizens, you're living in a dream world. No, they're just going to recruft their websites so as to generate HTML on the fly, therefore generating floating blocks, or DHTML popups. While not necessarily true popups in the strictest sense, they still will have the same function as the dreaded popups. So why don't we take care of DHTML popups then?
Because doing so programmatically would be next to impossible. There are too many ways that a clever DHTML programmer could get around any interpreter blocking code put in by the IE dev team. Thus you would probably end up with a code-bloated IE engine which didn't work 100% in blocking the DHTML. At the base of this too is the fact that DHTML, while annoying, does not take control of the IE window away from the surfer.
All in all, the popup blocking functionality is a welcome addition to a solid browsing application.