The New York Times talks about floater ads, the ads that are actually in the same window as the content. On the downside they’re harder to block than popups, but the silver lining is that you know which site they came from so you can stop going there.
Whenever I see a link to IGN or Site Point or some other ad-heavy site I get that feeling that I get when I’m about to click on a PDF; I ask myself “Do I really need to deal with the interruption?” Usually the answer is no. Now I can mentally keep track of what sites make money off of annoying me, and give preference to sites that see respect their visitors.
If I were Macromedia I’d be figuring out a way to stop this. Do they really want to be known as the company that brought advertising more annoying than popups? Look at how well it worked for X10.