Back when I used to work on WotC's advertising (in 2000-2002), we planned/placed some M:TG online campaigns for them. Even then we knew that pop-ups were intrusive and that people hated them, and yet the "click-thru rate" for the Magic Pop-Ups was many times greater than it was for the little banner ads. We had even higher CTRs for bigger, more dynamic ads that filled the user's screen while the page they actually requested was loading. I don't see those used as much any more. They were really expensive, anyway, so the Cost-Per-Click was higher than it was for the pop-up ads.
The key with pop-ups, as with any advertising, is to know who you're talking to. Some of those Magic players didn't mind the pop-ups, but we really only used them (for the most part) on really niche Magic fan sites. The people who went to those sites would often click on the pop-ups because the ad piqued their interest.
If, on the other hand, I was advertising that little spy camera and running the ad on a Magic fan site, well... that's a different story.
The key with pop-ups, as with any advertising, is to know who you're talking to. Some of those Magic players didn't mind the pop-ups, but we really only used them (for the most part) on really niche Magic fan sites. The people who went to those sites would often click on the pop-ups because the ad piqued their interest.
If, on the other hand, I was advertising that little spy camera and running the ad on a Magic fan site, well... that's a different story.