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ive read that sometimes google penalizes for using javascripts.
Bad or cluttered JS might adversely affect the spidering/ranking of your site, but I've never read of a 'penalty' for using it for legitimate purposes.
I believe AdWords won't take sites w/ popups, and I wouldn't submit to Yahoo with them active, and like Mohamed_E says, many users won't see that pop-up these days.
Look for the worst-case-scenario, which is: nobody will see the popup, and everybody hates them, and somebody might penalize for them someday, so come up with another catch.