I've always thought about it as well. Mainly I see tribalfusion (meaning from popular sites) or from fastclick. If most of your traffic is from links or search engine's, how bad could pop-ups be from a user standpoint anyway?
Well tribal fusion isn't just a pop up network... they do offer popups but they limit it to at most once every 8 hours per user. Pop Unders do really well cpm-wise, you just don't get to serve that many of them.
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