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I recently tried to help a friend disable their pop-up blocking, and we found four different ways that pop-ups were being blocked.
Back in March 2003 on the sites I could check, pop-ups were not working for an average of around 8% of visitors. I haven't measured lately, but I'd guess it's at least double that today. Fortunately, the programs seem to be getting a bit better and not blocking pop-ups that come from clicking on a link, only those that launch automatically.