Bear in mind that a lot of these 'fake' pop-ups require the use of Javascript.
If your users know what you are up to and turn off (or block Javascript) at your site, it may affect other aspects of your site.
In my experience pop-ups have a worse reputation than traditional banners... the sooner sites stop using them, the sooner more surfers will re-enable Javascript and be able to experience some very 'clever' sites to their full extent.
Just my 2c
Steve