If you are using IE, you could try running with "No Add-On's". This is an option that you can select by doing so:
Click Start -> All Programs -> Accessories -> System Tools, and then click Internet Explorer (No Add-ons).
If your problem stop's with just this, you should determine which add on is the cause, by re-enabling them one at a time.
If you are using Firefox:
In Windows, click Start, open the All Programs list, and navigate to the Mozilla Firefox folder. In the Mozilla Firefox folder, select Mozilla Firefox (Safe Mode). There are options there for reseting/ and disabling your add-on's specifically.
I personally use Opera, and I don't get pop-up's... ever. I'm probably lucky.
Whatever browser you choose is up to you. There are ways to fix em all.
Also, try running an AdAware, or Spybot - Search and Destroy to get rid of any extra unwanted material lingering on your computer. Running a good anti-virus is a great start, but having these extra programs, as well as running a firewall will help you to prevent further incidents from occuring.