Tree - Write documents in tree-like organisation with Markdown
Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.
TabNotes - Markdown notepad in your new tab
Boostnote - Boostnote is an open-source note-taking app.
Array - "Need a multi-user database application? Code it with HTML/OS.
Standard Notes - A safe place for your notes, thoughts, and life's work