Not all pop-ups are ads or even all bad. AdBlock Community Manager Rhana Cassidy explains the various types of pop-ups and how to block the ones you don't want to see (and allow the ones you do).
I'm going to have to break down the answer to this question into two pieces: first how pop-ups are likely occurring and second armed with that knowledge what you could do.
There's not really a question here. It's just an announcement of some hopefully helpful information I posted on AdBlock's Blog. :)
If you have a question, though, I'm happy to try to answer it for you!
AdBlock Community Manager
There are three ways to stop pop-ups in their tracks: your browser itself, dedicated pop-up blockers, and ad blockers such as AdBlock.