I made a plugin that allows you to make annotations while playing your game. The plugin remembers what you drew and wrote and imports everything into the editor.
When you run the game, you can press backslash to enter annotation mode. In my case, this unlocks the mouse. You can handle annotation mouse however you like, I have exposed a few values and signals that allow you to build your own custom behavior around annotation mode.
When you draw a stroke, and lift your mouse button, you are prompted to write an annotation. This stroke together with the annotation text are saved in the editor as nodes, allowing you to keep a “spatial to-do list” of sorts. You can change the annotation text however you please after creating the annotations, and since the annotations are nodes, you can transform and remove them however you want. Both 3D and 2D annotations are supported. I wrote this in one night, so bugs might still be present 
You can find the repository here:
Let me know if you have questions, or if there are features that you would like to see in this!