Ya, I mean just to reiterate what Larry said, you need to do all of the things he said. Also, get a good spyware detector. I recommend Spybot and Adware, both of which are free.
Pop-Ups: Some can be harmful, but mostly they are just annoying. I have the Google toolbar and it blocks virtually every pop-up that appear on sites. I've had it for about 2 months and the counter is at "1474 blocked". That's pretty good for a free program. Get it at
http://toolbar.google.com/
So...
Spyboy: Search and Destroy
Adaware
Google Toolbar