People can generally train themselves to automatically recognize and close the standard, reoccuring popup windows in less than a second. I’d say about 500 ms.
See, here’s the problem. Pop-ups are so cheap to put in place that even the tiniest response rate is still profitable. Extrapolating from personal experience is satisfying but not really an objective measure of their success. The website http://clickz.com/ has a lot of interesting material on web marketing.