Disabling Popups

I recently purchased a new home pc and in the in the first week something was downloaded that has plagued my system with continual popups whether I am on the internet or not. What ever is causing the popups starts up IE and goes to town. I’ve removed every program that I don’t recognize and the popups still occur. I downloaded a popup killer for a 15 day free trial. In 3 days it has killed over 3000 popups.
Any advice would be appreciated. I’m goin’ nuts!