When comparing Trilium Notes vs Zettlr, the Slant community recommends Trilium Notes for most people. In the question“What are the best knowledge base systems for personal use?” Trilium Notes is ranked 10th while Zettlr is ranked 12th.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Free and open source software
Pro Note encryption
Pro Excellent WYSIWYG interface
Pro Attributes that can be assigned to nodes and inherited
Pro Graph of node connectivity
Pro Note versioning
Pro Synchronization with a server
You can set up synchronization but you need a server to do this.
Pro Database storage rather than files
This enables the tool to do a lot of things that would be difficult with plain text file storage.
Pro Archival functionality
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 Interface can be confusing
There is a fair amount of flexibility to the interface but it can also become confusing, especially when some parts are not necessarily simple to use. Most of the basic features nevertheless are intuitive.
Con Database storage rather than files
This makes it a little less simple to work with (also has benefits).
Con Not markdown
It will import and export markdown but it does not store content as markdown. This isn't necessarily a problem if you don't need it.
Con Synchronization requires use of Trilium's sync server
This can be problematic to set up unless you have a web server that will support the requirements of this.
Con Obtrusive, like someone WITH CAPS LOCK ON
Too loud, too much going on, and definitely an in-your-face sort of feeling.