After having been around these note-taking apps for years, I'm still stuck with a directory of text and Markdown files. It's an obvious benefit not to be tied to one application developer's opinion of how to structure a note-taking application, and you can use any editor, Markdown viewer or static site generators to deal with input and output. Also, notes are just files, so there are lots of simple ways to synchronise them between systems (ssh, rsync, syncthing, even imap) and anything can edit a text file.

While some wiki functionality across notes would be nice sometimes, I still am not convinced to give up on the "raw data and bring your own tools" approach yet. Nowadays, most IDEs have across-file functionality anyway and there's a lot more choice and no lock-in going that way.