An option in the teleport menu to group different waystones together into folders or categories (Example: Farms, Houses, Nether, End, Overworld, etc.). This would be client side.

This idea reminds me of mine for tags, where you can create tags in order to group specific waystones together in separate lists.
This one is pretty much the same tho... so gonna like this one.

Optionally you should add two default folders/tags/groups:
Your Waystones - to mark all waystones you placed
Favorite - to mark all waystones you like using a lot. You could mark stuff like bases you are traveling a lot to.

I think it is cool idea, but I'd suggest images for categories, so you can either customise them better, or separate waystone names from category names. It would make that more atmospheric too