2 days ago i received a penalty on 2 large sites. ( it happent after i have added a second popunder ad, that was the only change but could be a coincidence).
the site was still present in google but traffic was down 90%.
I have removed the new ad and waited to see what happens, but today i received a manual penalty for "pure spam" on all the sites in my google webmaster tools.
Even domains that where parked for months received it.
The google empoyee gave a manual penalty for one of the sites and while it was there decided to give the penalty for all my sites.
One of the sites in the same niche and on the same server was not on the google webmster tools and its not penalized.
So if you want to protect your sites from penalties going to one to another just dont add them on the same google account.