After trying several open source desktop applications, I'm settling for Zettlr (for now).

Here are some things I like about it

• Notes are just Markdown files, and you can use folders to structure your notes however you want
• Like Typora or Mark Text, it shows a more or less formatted Markdown code, in a single panel. It's purely a matter of personal taste, but I prefer this to the approach used in many Markdown-base tools to show raw code & formatted preview side by side (it just feels very redundant to me)
• You can link between notes with drag & drop
• Tags are just #hashtags in your documents
• It supports Mermaid for generating flowcharts & diagrams
• It supports YAML frontmatter
• It has a lot of features to implement a Zettelkasten, which is something I plan to try out
• It does a good job as a Markdown editor
• It has a small pomodoro timer in the toolbar :)

Last time I tried, there were some annoying inconsistencies in linking to external resources (absolute/relative links).

And as an Electron app, memory usage can get a little high sometimes (especially compared to a PyGTK app like CherryTree)

Some notes on the other app I tried, for reference

QOwnNotes

Like Zettlr, it respects existing files hierarchies. In addition to .md files, it does use Sqlite for metadata (like notes tags).

It has a lot of nice features

• A web clipper browser extension
• User scripts
• Git integration (with commits at regular intervals)
• Customisable interface
• A small popup to select existing notes when creating a new link
• Tight connection with NextCloud/OwnCloud notes & todos

As mentioned above, I'm not a huge fan of editors using 2 panels for Markdown, and this is one of them.

VNote

It also reflects existing directory structure. It adds a json file per folder with metadata, something that can be annoying in some cases (like editing an existing folder).

Editing is done in a single panel that switches between Code or View mode. I might like that better than the redundancy of having 2 panels. But I still prefer the Zettlr approach.

Its search is maybe slightly more advanced than most, but beside that, has nothing special in my opinion.

MindForge

Interestingly very idiosyncratic. I think it definitely reflects its author's own way of working, instead of following standardised UX approaches.

I enjoy the vocabulary used: the File menu is “Mind”; you don't “Save”, but “Remember”; “Settings” are “Adapt”, etc.

But beside that, it doesn't really work for me. I find the interface way too convoluted, with simple actions taking a lot of clicks.

It has some interesting features, like suggesting related notes, and a concept of Importance/Urgency.

While most apps create a new Markdown file for each not, MindForge gather all notes of a “Notebook” inside a single file, using Markdown headings and metadata in comment tags to separate the notes.

Boostnote

A very polished app that also has a web version (which, as you can imagine, comes with paid plans to expand storage).

It has some coders-friendly features, like reusable snippets, and something similar to Gists – a note that can store a variable number of sources “files”.

I'm less a fan of the way notes are structured and stored. You can create different “storages”, but from there it's a flat list. While you write notes in Markdown, they are actually stored as CSON files, all in a single folder, with an ID as the filename.

You can switch between a traditional 2-panels mode, or a single panel mode that switches automatically from “Code” to “View” when the focus is out of the text field.

Joplin

Joplin is pleasantly well designed.

Some cool features are

• “Todo” notes : notes with little checkbox next to their name in the notes list
• Built-in support for file synchronisation (including Webdav and local folder)
• E2E encryption
• A web clipper browser extension

Sadly, 2 panels again, although it has an “experimental” WYSIWYG mode.

While it uses the Markdown syntax, your notes are actually all stored in a Sqlite database. So not what I was looking for.

But also

I also briefly tried Simplenote, Notable and PileMd, but for some reasons I forgot, it wasn't suiting me.

While writing this, I also found back Standard Notes from my bookmarks. Leaving this here for whoever is interested, but I'll stick to my Zettlr plan for now ;)