Do pop-unders affect ranking?

Matt's answer:
Matt Cutts: Biz in the USA asks an interesting question. He says, ‘We got rid of a profitable pop-under ad (since we thought the concept was user unfriendly)’ — which I agree with – ‘but then pages-per-visit and time-on-page dropped – along with our rankings. Does Google reward or penalize for a pop-under, directly or indirectly?’ To the best of my knowledge, we don’t either reward or penalize in any sort of way for having a pop-under or a pop-up or anything like that. Users don’t like it so it could be that users are not linking to your site as much or they thought that your site was lower quality and so they’re telling their friends not to go there. But to the best of my knowledge – and I’m not familiar with everybody and every single thing in search quality – but I don’t know of anything where we would say, ‘Oh this site has a pop-up or a pop-under so don’t rank it as highly.’ It’s a common feature request. A lot of people want us to do that. But to the best of my knowledge, we’ve never done anything like that.
by Matt Cutts - Google's Head of Search Quality Team