I imagine that quite a few people run phpAdsNew or banner rotation scripts with similar features. One such feature is to block/display promos according to user agent (ZangoToolbar) which can be useful in this particular fight.
Estimates as to how many PC's are infected with scumware seem to be running from about 0.5% to 3% for Zango alone (and there are 20+ similar scumware installers). That represents a heck of a lot of surfers, although obviously leaves room for overkill. I have seen some people suggesting blocking/redirecting infected surfers completely and I think that definitely qualifies. I'm dubious about the effectiveness of most of the warnings suggested, because they not only require the surfer to believe you and care, but also he must copy a URL into an address bar (possibly the very one in which he was viewing your site).
The point is that not every promo on a page is going to make a popover appear, therefore it seems like a good first step to install scumware on a spare PC and check your sites to see which promos are affected. Then either swap them for others which are not, or if you have the right banner software, set it to show "infomercials" in place of affected promos to infected visitors.
Written to sound sincere and not as if they are selling something or offering something as bad, they could be as effective as alerts and I suspect if someone has voluntarily clicked a link, he will be more likely to follow the suggestions made on the page to which you send him.
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