Pop-up is a type of windows that appear over the browser window, while pop-under is is a type of windows that appear behind the browser window. - Dynashox -
You've already been told of the difference of "-up" and "-under", and that they're both annoying, but unders are more annoying than over because they can't be killed by a swift alt+f4.
Perfect! They both are annoying and what's more annoying is that some sites use modal pop ups where you will have to act on it to continue. I just fail to understand the reason behind this kind of advertising. Most of the times the windows doesn't even load fully before its closed.