The popups are extremely common on torrent sites, illegal video sites, porn sites, and many other less than reputable sites.
Even some reputable sites use popover ads - personally, I try to remember those and refuse to visit them anymore.
Don't know how she did it, but, after almost 7 years of being free from such nuisances, my wife somehow managed to install Geneio on her iMac a couple of weeks ago. Likely from Facebook or one of the games she downloaded had it included in the installer.
Several of the application download sites are now including adware along with the application you want - including Cnet's download.com and others.
Don't know if Adobe is still doing it, but they were packaging 4-5 pieces of adware with Flash for awhile.
Have to be careful everywhere.
And there's not an anti-virus made that will protect people from those phoney-baloney browser adware toolbars.
Still imho, the only thing really required in OS X, is "know" what you are downloading and installing.