I have used ad-aware, SpySubtract and Spybot Search and Destroy. Of the three programs, Spybot does the best job of automatically intercepting tracking cookies and malware preventing them from being installed in the first place. The other programs require you to remove them after they have installed.
This site persistently tries to install Avenue A Inc cookie. Everytime I click on a message or respond it tries to install and is blocked. For popups, I use AdSubtract pro, and don't ever get popups. Try the spybot S&D if you want to intercept trackers and spyware, and AdSubtract to kill popups.