Protesilaos Stavrou (Prot) has published an excerpt from a conversation he had with someone asking his advice on Emacs and note taking. The TL;DR is that his correspondent is a Vim user who is considering changing to Emacs for the advantages it offers for note taking. He is asking Prot how to proceed.
Prot’s advice is eminently sensible: Start slow. Use Org mode to begin with and add other packages only when you find you need them. Specifically, he advises using a single notes.org file with a heading for each note. Each note can have, or accumulate, additional subheadings as required. He also recommends setting the file to open with only the headings displayed. Folding is one of the strengths of Org mode and helps keep you from being overwhelmed by the available information.
His best advice—in my opinion—is to concentrate on the notes themselves rather than on the mechanics of taking them. He encourages note takers to spend time on writing purposeful and coherent prose so that when you read them later you will understand what they’re about and what your thinking was at the time. He also suggest linking new notes with previous notes where it makes sense. That, of course, is the basis of the Zettelkasten method, which Prot says he hasn’t studied and doesn’t necessarily recommend unless you, too, are genius workaholic like Niklas Luhmann. Better, he says, to start slow and find a system that works for you.
If you take notes, in Emacs or elsewhere, you should definitely take a look at Prot’s post. It has a lot of good advice without insisting that you use a particular piece of software.