I have a program called AdSubtract Pro.
http://www.intermute.com/products/adsubtract.html
I have had it for years and I believe it helps a lot on keeping my computer clean.
They have a free version with limited features, and a Pro, shareware, version with expanded features.
I started with the free version years ago and was so happy with it that I purchased the shareware version. I have not had popups since I first started using it. And the shareware version keeps track of the cookies websites put on my computer, and gives me the option to do whatever I like with them. Some, like this site, I "Protect". All of the rest get deleted next time I start the computer. When I turn on the computer each day, only the "Protected" cookies are there. from my "Trusted" sites.
It also allows me to clean the various History's, Temporary files and Browser Cache as well. I like my History's so I keep them.
Edited to say:--Be aware tho that if you let Windows clear your cookies, it will delete even the ones you wanted to keep.