I used to use a program called MyIE a while back, it's now called
Maxthon. It has a Ad Filter/Popup blocker. Very effective when i used it and easy to add sites or source sites of ads/popups to the block list.
It uses the IE engine, so i never had any probs rendering websites, worked exactly same way as using IE normally.
I'd recommend it as worth a try if you've time. Takes a little getting used to, and i disabled the skin feature straight away.