(This is not my main computer, so it may be a while before I can respond)
Are the popups labeled "Messenger Service"?
If so, use a firewall, and block UDP port 135. Some people are using this port to send spam to Windows boxes. These popups look like a normal grey Windows dialog box.
If they are normal web popups, then you will need a popup-blocker program or turn off Javascript. Some sites will popup ads immediately after you close your browser.