Love them or hate them, popup killers are here to stay. But what strikes me is that sites relying on popups for content are not testing their sites properly with a popup blocker. On this site for example non essential content popups are used.
Popup killers take many forms. Some will only kill onload/onunload popups some will kill everything except target="windowname".
Popup killers can also prevent flash movie external links from working. I'm not 100% sure what flash uses for opening new windows - perhaps its an actionscript thing. All I do know is that some flash movies don't open external links when a blocker is used.
Remember your site is useless to some visitors if you do not consider the effects of these applications. I know you can't account for everything on the web but why make life hard by using fancy gimmicks that can do more harm than good.
Here is 1 I use for testing, they are free and don't contain spyware.
Popup killers don't care if it's an ad or content, if you open a window in a way it doesn't like then say goodbye to your visitor seeing your content.