12Ghosts Popup-Killer LE 7.02 is free for non-commercial use, which is a good thing because this is worth having a look at.

Just like the name says, Popup-Killer is a pop-up killer; although rightfully it should be called pop-up preventer. It completely blocks pop-ups that are spawned through javascripting or HTML links. You can ‘allow’ pop-ups by placing them on an approved list, or by holding down CTRL. On the same note, since it can play a sound when a pop-up is blocked, you can ensure that important pop-ups are not disabled.

12Ghosts Popup-Killer does a lot more than just block pop-ups. It cleans IE’s temp-file-droppings, history and your Windows-file histories as well. It can also block off the Windows Messenger service.

A cool boss-key option lets you hide any application from your screen and taskbar.
Furthermore, it features a toolbar that can work alongside the Google toolbar. This has a useful image-toggle, an always-on-top button and you can register a site as ‘approved’.
It does require some initial configuration, and this could have been made a little more intuitive. There is an ‘options’ tab under a ‘settings’ dialog box; there is also a ‘general’ tab which features, well, more options. Don’t get us wrong -- it is amazingly versatile, but you need to hunt around for all the features.