There are 4 things I do to prevent this problem:
1. I use Glary Utilities (http://www.glarysoft.com/) which has a Startup Manager that allows me to disable any applications that I don't want to launch automatically with Windows 7.
2. I followed the suggestions at http://www.tweakhound.com/tweaking-windows-7/8/ to disable as many Windows or application services that I don't need, which may automatically start up with Windows 7.
3. I use Malwarebytes Anti-Malware Free Edition (https://www.malwarebytes.org/free/) to run regular scans which should capture anything that is causing the pop-ups. Glary Utilities mentioned earlier will also do a cleanup of registry and other unwanted software.
4. I use Bitdefender Antivirus Free Edition (2014) (http://www.bitdefender.com/solutions/free.html) for real-time virus protection. Malwarebytes Pro also has real-time spyware/malware protection but I don't need to run both at same time, and Bitdefender Antivirus Free Edition (2014) uses the least memory.