NoteKit is described as 'This program is a structured notetaking application based on GTK+ 3. Write your notes in instantly-formatted Markdown, organise them in a tree of folders that can be instantly navigated from within the program, and add hand-drawn notes by mouse, touchscreen or digitiser' and is a Note-taking tool in the office & productivity category. There are more than 100 alternatives to NoteKit for a variety of platforms, including Mac, Windows, Android, Linux and iPhone. The best alternative is Joplin. It's not free, so if you're looking for a free alternative, you could try Standard Notes or Google Keep. Other great apps like NoteKit are Notion, Microsoft OneNote, Evernote and Simplenote.
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, can be copied, tagged and modified either from the applications directly or from your own text editor.
Zettlr is a supercharged markdown editor that combines many writing editor features and collect them in one application. It aims at speeding up your workflow and help you write without any interruptions.