'autoruns' is a good util that can prevent some malware from loading on boot.
if its more serious, 'combofix' should fix it, but you'll need an expert for that.
If you have another PC with both hardware and software which can create a bootable image on CD/USB_Stick I recommend that you run Microsoft Window Defender Offline from a bootable CD/USB_Stick: What is Windows Defender Offline?
install mbytes anti-malware and do the scans ... google mbam.exe downloads ... if still an issue -- reinstall the os so you have a clean device from the start ...
I'm a big fan of MalWareBytes and Bit Defender but find these often don't detect AdWare. If I have a system with out of control pop-ups then my weapon of choice is SuperAntiSpyWare (Google that). They do a free version which will list all such "threats" and asks what you want to do with them. I normally let it nuke the lot (don't be surprised if it finds several hundred "threats").
Would you consider Avast too? It's a good free tool.
You haven't been visiting naughty sites have you? :o They have a habit of installing pop-ups, (and diallers in the olden days) or setting your web-pages to be always opened through their site and then they can pop-up some more. I got hit by going to a mis-typed address once. It took me ages to get clean again.
If you do go with Avast, run a full scan and a deep level boot scan. Leave it running overnight. It's not quick, but it is good. As a one off, you can also use AVG, but that requires registration after a short period and then wants you to pay too. You can always uninstall it after a full scan.
Anway, isn't this a Unix forum? Ho hum, we all have to live with Windoze, so let us take away as much pain as possible. Any other suggestions?
Check the list of programs in Add or Remove Programs for anything suspicious. Then check your browsers list of add-ons and delete anything you dont use.