Are these popups, regular popups or actual spyware related popups? If it's spyware related, using a program probably won't help. If it's a regular popup, you can try using a browser like Mozilla Firefox. It has built in popup blocking features and is much more secure than using Internet Explorer.
If the popups are spyware related, then do this:
Run a new HijackThis and Panda scan. Post their logs here.