If you have a popup blocker running and you're still getting popups, this tells me two things:
1. You're probably using Internet Explorer.
2. You've probably got some kind of adware, or similar malware, on your system.
There's no such thing as a system that will both allow IE to reach the web and perfectly protect against IE-targeted spyware and adware. Because of IE's hooks deep in the Windows operating system, there is essentially a direct pass-through between webpages you visit and your operating system. This allows your browser to perform certain administrator-level actions, both on the system in general and more specifically with applications to which IE has direct access (which generally includes at least those Microsoft applications that are web-enabled).
I recommend you get Bazooka from kephyr.com, Spybot Search and Destroy from safer-networking.org, and Ad-Aware from lavasoft.com, and use all three of them to scour out your system (in addition to using whatever antivirus software you have to double-check for virus, worm, and trojan activity). If you're on a corporate machine where you're not allowed to install software, let your IT department know that you think you might have picked up some malware and would like to get it cleaned up.
You might also look into getting the Firefox browser from mozilla.org, which is essentially immune to the sort of malware that you're probably suffering through. Again, that could be difficult to arrange if you're on a corporate intranet.