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I think Pop-Ups are here for a long stay... very very long stay.
Maybe, but the longer they're around and the more they're used, the more incentive ISPs and software manufacturers will have to combat them--if only to gain a competitive edge in the marketplace. Earthlink is already offering a popup killer to its subscribers, and Norton Internet Security 2003 includes an adblocker that (according to the Symantec Web site) "now stops even more banner ads, pop-up windows, pop-under windows, and other Web distractions."
I suspect that, over time, popups and other intrusive forms of advertising will be productive only for advertisers who are targeting unsophisticated users--i.e., the kinds of people who don't even use antivirus software. If those people are your target market, maybe a popup ad will become the perfect advertising format. ("If you can see this ad, you need Norton Internet Security.") But for advertisers who want to reach a more educated or sophisticated audience, pop-ups are likely to become less productive (and maybe even a waste of money because they reach the wrong audience).