I hate pop-ups, some people think they are usefull. I think you need a really good reason to present in your website a pop-up. A commercial reason to attrack more attention, noway. Be more creative to get a hit! A functional reason for navigation, no. Read all studies about usability and you’ll discover people get lost with it
Only exceptions are: an enlargement of a picture or use it if you want to give a quick hint, a tip, a calculator or a question. Rule is that a pop-up appears fast and should dissapear even faster. I’ve used a script where the picture enlargement pop-up goes away automatic after clicking somewhere outside the pop-up (here an example, click on the pics). Google has made it clear why they are not using any pop-ups: No Pop-up Ads on Google .