When comparing Tomboy vs Zettlr, the Slant community recommends Tomboy for most people. In the question“What is the best cross-platform note-taking app?” Tomboy is ranked 14th while Zettlr is ranked 49th. The most important reason people chose Tomboy is:
All the components are free, opensource, and allows self-hosting the sync server.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Free and open source
All the components are free, opensource, and allows self-hosting the sync server.
Pro Can be extended with add-ins
If Tomboy doesn't have the features you want out of the box, you may be able to find them here as a plug in.
Pro Lightweight
Pro Focuses on writers
While many Markdown editors don't offer specific support for a certain type of workflow, or offer features for scientific workflows only, Zettlr offers features that help the writing process of journalists or researchers in the arts and humanities. It's a lot more text-focused than most editors.
Pro Citation support
While it supports a diverse range of syntax (chart, easy image insert, etc.) found in other editors, the great citation support made it possible to write real articles. Citation from Zotero and Mendeley can be inserted easily which is a huge plus.
Pro Almost perfect
This is the best option, still not perfect, there are some bugs like creating / editing tables and resizing images, but the PROS destroy the CONS, easy quotes, WYSIWYM , attachments tab (supports attaching and opening links to any file), table of contents, TAGs, easy hyperlink between files (same as citations), export to many formats (like Word, HTML5, PDF)...
Pro Renders math in-place through KaTex
Cons
Con Can't easily install on Windows 7
Con Obtrusive, like someone WITH CAPS LOCK ON
Too loud, too much going on, and definitely an in-your-face sort of feeling.