These are sent using the Messenger service integrated into Windows 2000 and XP (try the net send command to see for yourself).

To disable the Messenger service, go to Start → All Programs → Administrative Tools → Services. In Services, click on Services (Local), then on the right side, find Messenger and disable it.

Note: not everyone will have Administrative Tools in the Start menu. You need to make it visible under Taskbar and Start Menu Properties (right-click on taskbar → Properties). The safest way to get to Component Services is to enter %systemroot%\system32\com\comexp.msc into the command line.