Ad-Aware does I lot more than stop popup's, it's their to detect and remove malicious programs that's infected your Computer.
A standard list of recommended software/Hardware to help protect your privacy and Computer are:
1) Ad-Aware - Adware/tracking detection and remover
2) SpyBot - Spyware/Malware detection and remover
3) An Anti-Virus program: Most use AVG Free edition
4) CCleaner and Glary Utilities
5) Hijackthis
6) Rootkit detector like F-Secure BlackLight
7) A Hardware Router to help prevent direct infections/attacks from the Net
I go down a slightly different path, I have all the above software/hardware but when I'm online I use VMware which protects my main operating system from getting infected by any malware,adware,spyware etc.
Take a look at free software like virtualbox for windows or pay a small amount for VMware, just Google them for more information.
Encryptor
Linux rocks the planet...