The Waypoint Display is a small window which shows the active waypoints in you datapad. Each entry contains the name of the waypoint, its distance from you, and an arrow pointing to the waypoint location. There are several options on the waypoint page of your datapad to control the contents of the Waypoint Display.
If you right click on the Waypoint Display, a list of all displayable waypoints is shown with a "[x]" in front of the active waypoints. Clicking on a line in the list toggles the waypoint state between active and inactive. Active waypoints are visible in the world and show up in the Waypoint Display.