Since you haven't got an answer in six hours I'll provide my unqualified thoughts on this subject.
I'd say that a popup is a modal window, possibly with the specification that popups are limited to simple interaction such as information, yes/no questions or one or two text input fields.
There is at least one web designer who disagrees with this, but I wonder if he really read the Wikipedia page he's linking to.
Edit: come to think of it, not all popups are modal.. but that's probably because of a misunderstanding of what a popup should be.
Edit 2: fixed the link