Had a site that was ranking in the top 3 for competitive keywords, that took a -20 penalty back in Feb 2012. There were no warning in webmaster tools etc... I have tried everything to recover this site, but it seems to just sit where it is on 3rd or 4th page. I was just thinking, the site has a single popunder on every page (including the homepage). The popup brings up an affiliate page. Does anybody know if popups can affect your serp position?