Safari 6 (OS X Mountain Lion): Why block pop-up windows?
You can set Safari to block pop-up windows, which some websites use to display advertisements. However, you might miss important information if you block pop-up windows. For example, a website might use a pop-up window to request your user name for services it provides.
Blocking pop-up windows stops only those windows that appear when you open or close a page. It does not block pop-up windows that open when you click a link on the page.