Org-mode is especially great for people who like branchy outlines as their notes. It allows to jot down a note quickly and to move them around in the tree as the heart desires. I have thousands upon thousands of notes, mostly short one- or two-sentence long.
Plus both Emacs and Orgzly allow some programmatic fiddling with the notes.
The downside is that copying anything with links or formatting out of Org requires converting its markup to Markdown or whatever.