I've begun to receive regular requests from my clients for "pop-ups," alternately called "pop up windows" or "you know, a little box that comes up with some extra information?"
I don't like them. I don't like them at all.
That said, as the consultant and designer that my clients have hired to make their web site visions into realities, it's my job to do what they want -- in part. Another part of my job is to steer them away from the technologies that might do them a disservice. I tell them not to host with their brothers-in-law who just opened a hosting company in their basement; I suggest they avoid flashing yellow "NEW!" buttons in front of each new blog post; and I tell them, gently, that there are other ways of making a piece of content "pop" without making it "pop UP."
Here are some of the reasons why I recommend against using pop-up windows.