Yeah this is a very useful feature of the user notes, a few improvements can be made like being able to sort them by date or by alphabet and search for a particular note/text, then it will highlight it and you can drag it out or copy directly from message center.It would be very convenient to have this feature on the map itself, but until then you can use the Notes feature in the Message Center to keep your waypoint links, even with comments.
My solution:
Step 1:
Open Message Center
This can be done by clicking the blue icon near the top left corner
or by pressing a costumized icon or action key to create this
Press L (default to get Edit Panel)
Press Y (default to get Action Library)
Search for Message Center
drag the Message Center to the screen.
(If you also need a action key)
Press G (default to get Keyboard Map)
and drag the Message Center icon to the desired key.
Step 2:
Create a new Sticky Note
This action is made by clicking on the top left corner of the Message Center window (with a left click it show the options: Mail and Sticky Note
Step 3:
Put the information that you want to save in it
For example:
Open chat and write:
/pos
this will get you a link for your current position
then from chat Copy Waypoint Link
Go to the sticky note in which you want to save this information
and paste it (right click in the note field or Ctrl+V)
Put a small description/meaning on why this coordinate was saved
It is useful that the first lines of the Sticky Note to contain a description of what it contains
You can also costumize the color of the note (option for it is next to delete it on the top left corner)
Step 4:
Minimize (top right corner of the Sticky Note)
So that it doesn't occupy screen space
Step 5:
Reopen the Sticky Note to read it or add new informations
(Open Message Center and choose the sticky note that interests you, the first lines that you made to describe its contents will help you with this).
It also helps to Toggle so that only:
viewing of costume notes is active
(Globals and auction will create many lines and make reading of old notes hard to achieve)
This way you can save thousands of waypoints with a detailed description of their meaning.
(To put the waypoints back to Map just right click on them and select: add waypoint)