Do these "pop-ups" that are appearing have "Messenger
Service" in their titlebar? If so, what
you're seeing is the Messenger service built-in to
Windows, *not* Windows Messenger (which
are two different things) which spammers are exploiting --
this is not Microsoft, nor can
Microsoft control them anymore then they can control spam
to your e-mail inbox.
To get rid of these pop ups, you'll need to disable
the "Messenger Service", click Start,
then Run, enter "services.msc"and click OK. Scroll down
to "Messenger", select it,
right-click and then choose Properties. Under startup
type, choose 'Disabled' and then
choose the 'Stop' button. After the service is stopped,
click OK. Nothing in Windows or any
real third-party applications should be effected by this.