I have only used Safari and, for a long time, it has had a "Block Pop-up Windows" feature.
The trouble with the "Block Pop-up Windows" feature (which, as you say, Safari has had for a long time), is that it doesn't always work. It still allows JavaScript to create a new window in response to a user click on something on the page. In effect, all it blocks is windows that are "popped up" by JavaScript that runs as part of the page load (before there's anything to click on) or in response to timers.
Case in point. There is a website that I used to visit frequently to view comics. I had "Block Popup Windows" enabled, but going to the site only shows the first comic I've subscribed to. To see the next, I would have to click on what is in effect a "next comic" button. That click gave the site permission to open a new window, almost always as a "pop-under", despite my preference.
I found that disabling JavaScript before going there worked wonders. I eventually stopped going there altogether, which works even better.
I notice that Safari 6.0 no longer has the option. Apparently it's always on now. I just checked in at that site, and didn't get any pop-unders this visit. (But then, I didn't always. They were clever enough to only occasionally give you one.)
