The best that I've used is PopUpCop. With no configuration needed it's very effective at blocking the advertisement pop ups while allowing most legitimate pop ups that are needed for site navigation. For the occasional site that doesn't work properly, it's easy to disable it altogether or add the domain to an "allow list". My experience is that it just works 99% of the time without having to fuss with it. You can also choose to disable all sorts of other web annoyances like background sounds and window resizing.

It's an IE plugin and not a proxy or seperate app that has to watch for window titles. The only downside is that it costs $20 but is well worth it, IMO.

-Dylan