NotePlan - Make plans inside an individual markdown note for every day in your calendar. Use it as a journal for your daily tasks and plan todos in advance. For Mac, iPhone and iPad.
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.
Mochi - Write notes and flashcards with Markdown and study them with spaced repetition.
Boostnote - Boostnote is an open-source note-taking app.
Markdown New Tab - Write notes in Markdown directly in the 'New Tab' page
Standard Notes - A safe place for your notes, thoughts, and life's work