In my case, popups appear regularly in Safari even if block popups box is checked. Granted, the number of sites that do this is small, but it is still annoying. The most glaring example is travelocity.com. Try to type in flight credentials on the main page - and a popup appears. This is why I shop but do not buy on that site.
There are also a couple of other web sites that would throw a popup once in a while.