In Media Sites: Say No to Pop-Ups, I don’t think Adam Penenberg spent enough time on one point:
One survey conducted in 2004 by Bunnyfoot Universality, a U.K.-based web consultancy, determined that as many as nine out of 10 users who clicked on a popular pop-up ad were really just trying to get rid of them and clicked through by accident ‘because the close button was so difficult to find.'”
This means that pop-ups are essentially click fraud. If you advertise online and you buy pop-ups you are most likely overpaying. Nine out of ten accidental clicks means you could be paying 10 times too much for pop-up ads, for clicks that won’t do anything for you.
Don’t take my word for it, take a look your logs. Compare how long a visitor from a pop-up ad spends on your site with how long a visitor from an in-page ad sticks around. I’ll bet most of the pop-up ad people close your site before all the images on your page load.
[Update 2: Adam Penenberg posted a comment apologizing and saying that “the ‘money side’ of the house is investigating the matter.” There is generally a separation of editorial and advertising in news organizations and while it was kind of embarrassing in this instance, it’s a good thing to have a wall between the two. While it prevents a writer who bad mouths pop-ups from keeping pop-ups off their own article, it also prevents an advertiser from telling a writer what they can and can’t say about the advertiser.]