Over the years, growing numbers of Web sites have been designed to include pop-up windows that are not advertising and that users may consider helpful rather than annoying. These legitimate pop-ups - like calendar updates and explanations of new navigation features - enable designers to alert visitors to news without substantially revising the home page.
I for one find any pop-up annoying. I have never seen a helpful pop-up and consider them all "illegitimate". In the good old days before Javascript, I found it much easier to locate and extract information from websites. Now that everything is hover-over-this and pop-up-that, it is just getting impossible to navigate sites efficiently. I wish web designers would offer a no-Javascript no-Shockwave just plain old HTML version of their sites. Then I can click my way to the information I want without the eye candy getting in the way.