On the Main Map screen of GaiaGPS.com, click the Waypoint icon to drop a pin.
First, click "Create Waypoint", then click the map to add waypoints.
You can manually move the waypoint icon by clicking it,
Once you've clicked the map, a waypoint icon will appear, and a tool box populates on the left. It looks like this:
A. Custom Waypoint icon selection (GaiaPro only)
B. Waypoint name generator (which provides a list of automatically generated names based on location, including coordinates, but can be manually changed as well)
C. Delete waypoint icon
Add notes and save your waypoints here, too.
Once you've finished creating your waypoint on the main map screen, you can find them in your saved data on the site, as well as on your device once you've synced.