The Messenger Service has been around a long time. It is used for network adminsitration and monitoring and for devices to talk to each other.

The reason the pop-ups started is that spammers found a new avenue. Email spam gets blocked and nobody looks at web pop-up ads so they discovered that many firewalls allowed Messenger Service traffic through and that by broadcasting a message using the Messenger Service they could hit computers directly with an official looking message rather than waiting for you to check your email or surf the web.

You can disable it by right-clicking on My Computer on the desktop and select Manage. Expand the Service and Applications tree in the left pane and select Services. Locate the service called Messenger and right-click it to go into its Properties. Change the startup type to Disabled.

From now on the service won't be able to start. You can also stop the service by right-clicking on it.

Hope that helps-