I recommend Boostnote. Boostnote is an Open source note-taking app for programmers. It focuses on writing Markdown note and code snippet quickly, can organized in a better way. You can sync data to multi-devices(Mac, Windows, Linux, Android and iOS) via Dropbox.
■ Download https://boostnote.io
Take a look at RedNotebook:
- Supports a variant of Markdown
- Can include links & images
- Stored as plain text, backup as zip
- Various search and organiser tools
- Cross Platform - Linux, OS-X & Windows, even portable.
- Free: Gratis & Open Source (GPL)
- Spell Check
- Export to plain text, HTML, Latex or PDF
You should take a look at Laverna. I don't know how well it covers your "organizer" requirements, but it:
- Supports Markdown
- Is cross-platform (Linux explicitly mentioned, also windows etc)
- Supports encryption
- Is (can be?) self-hosted and locally stored
- Free and open source (on Github)
NOTE Although it works for me (better as a note taker than note organizer, however), I observe in this question An open alternative for Evernote? that some people are having issues with Laverna when they attempt to use Dropbox for synchronization.