If you’re the type of person who likes to annotate files but keep your notes external to the file itself, you may be interested in nobiot’s org-remark. There are a couple of videos [1, 2] that show how it works and some of the features. There’s also a user manual that describes its features and how to use them in detail.
The TL;DR is that you simply select some text and org-remark highlights it and opens a separate window in which you can make notes. You can also open existing notes corresponding to an already highlighted area. There are different colored “pens” available for highlighting text and you can define others if you need them.
All of this is demonstrated in the videos and explained in the users manual so take a look if you’re interested. I have no need for this capability but lots of people do. If you’re one of them, take at look org-remark. It’s available from the GNU ELPA repository or, if you’re adventurous, the GNU-devel ELPA repository for the development releases.