Their are two types of popup adverts. Traditional popup adverts are a big no. If you have these you will be penalized. Overlay or floating adverts aren't technically pop up adverts and are different as they are harder to determine. They are usually divs inside the page themselves and therefore not as bad.

One thing to note though is user experience. If you increase your bounce rate or reduce pageviews due to the annoying adverts Google will find out and penalize you that way.

These have more to do with the "page layout algorithm" which you could read up on than Google Panda