When comparing Gingko vs Zettlr, the Slant community recommends Gingko for most people. In the question“What is the best cross-platform note-taking app?” Gingko is ranked 21st while Zettlr is ranked 49th.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro You can customize colors
Pro Allows focusing on one piece of information at a time
Since Gingko documents are "trees", they are always organized on the go. And since everything is written in cards, it is possible to focus on one chunk of content at a time.
Pro Easy to overview
Despite the complexity of the tree structure, it's always clear where you are, and how to quickly add your thoughts.
Pro Markdown support
All formatting is done via Markdown.
Pro Non-linear
Non-linear notetaking allows you more flexibility, freedom and creativity.
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 Limited free version
The free version is limited to 100 cards and 10 documents. Depending on how you use it, this might not be enough.
Con Obtrusive, like someone WITH CAPS LOCK ON
Too loud, too much going on, and definitely an in-your-face sort of feeling.