I’ve fallen deep down the Silverbullet rabbit hole. Self hosted markdown editor but with built in dataview style querying (if you used Obsidian that will be familiar), accessible cross platform and with a progressive web app, and basically endlessly extendable with a scripting language. Really really enjoying it and it’s made me finally move from Obsidian, which I used to evangelize (and pay for the premium sync features). Definitely check it out. Silverbullet.md

You sound like me from last month. I strongly recommend silverbullet, check it out on https://silverbullet.md

• Can be selfhosted

Check, even has a simple docker compose

• Stores the notes as plain text or *.md files, not some SQL database.

Check, it does have an SQL database, but it's used for queries, you can even copy or modify MD files at will

• Can use Marddown format.

Check, it's a superset of markdown that includes queries for cool stuff like create tables that group data from other pages

• Have an android client or at least a mobile optimized web-interface.

Check, it has a PWA that works offline and syncs when back online. Note that this means that all files will be on your device if you use it like that, but that's expected.

• Not a must but it would be nice to have a to-do list option.

Check, like I mentioned you can query all tasks on all pages and even do filters based on several factors, like where the task is defined or extra attributes that you set to them, e.g. priority.

Edit: bonus points:

• The main developer is active here https://lemmy.world/post/11816898
• Also he's very active on discord and always answering questions
• Easily extensible with plugins and simple JavaScript functions, e.g. very easy to write a function to import a section of a page
• You can have multiple instances in sync with syncthing (just exclude the databases from syncing)

Obsidian + Syncthing is what I’ve settled on. Not perfect, but the best I’ve used.

Nextcloud with the "Notes" plugin and app.

https://nextcloud.com/blog/nextcloud-notes-secure-note-taking-integrated/

https://github.com/nextcloud/notes

Nextcloud Notes is pretty good. Btw Joplin has an option for End-to-end encryption.

Obaidian + Syncthing will do the trick.

I use Obsidian, you have mentioned it and it’s not self hosted, but for me that depends on how you look at it. I use it in a folder that’s synced to Nextcloud, so I consider the data self hosted markdown files. The viewer, i.e. the Obsidian app is not self hosted, but I consider that just a client used to view the data so it doesn’t really bother me.

I'm self-hosting Obsidian as described below and it works really well. The syncing happens automatically in the background and I rarely encounter conflicts. I'd highly recommend it! https://avidandrew.com/elevate-your-note-taking-with-obsidian.html

Obsidian + obsidian git plugin

Logseq has an Android app and clients for the usual desktop platforms. It stores as .md files. It meets your requirements. I'm not sure why you're focused on Firefox support?

One I have my eye on is Silverbullet.md. the creator recently promoted it here and it has some nice ideas. It's a web app that you self host. Behind the scenes everything is stored in .md files.

I use logseq. It has an Android app, and also desktop app (the latter being more complex). Also, it's plain markdown.

But you have to sync the different devices yourself and be careful not to run two instances at the same time.

I already replied to a different thread, but figured I'd comment on some of the other options too. My vote is for Silverbullet, but I've tried way too many note taking tools.

• Joplin: I ran into multiple syncing issues that caused data loss and large numbers of conflicted files. I'm pretty sure these were all fixed a long time ago, but it was annoying. The dev was always good about fixing issues when they came up. It takes forever to sync on my devices and only syncs while the app is open with the screen on. The format it exports markdown files in isn't standard, so I had to write my own scripts to export from joplin to markdown and preserve metadata.
• Standard Notes: I was willing to pay for this, but it's extremely slow. Their support said it's because it loads everything into memory, which I'd expect to be terrible on mobile with large databases. It's also pretty limited in what you can do on the free self-hosted version.
• Obsidian: I really like obsidian's ui/ux, and my only complaint is that it's not OSS. I'd even be happy if they offered a self-hosted sync solution. There are some third party solutions for syncing, but they aren't as smooth as the paid sync.
• Trillium: I love Trillium. I would vote for it, but it recently entered into maintenance mode. The community is working to start a new fork and I'm sure it will be great, but it's too new to know where things will go yet. Trilium lets you encrypt specific notes and also has a cool plugin system where the plugin scripts are just notes in the database. It does have a mobile interface, but it's a bit limited compared to the desktop interface and also doesn't have an option to sync notes to use offline.
• Silverbullet: My current choice. I use it between windows, macos, and an android phone. I leave all three clients on sync mode all the time. The interface is minimalistic, but offers everything I need for notes and documentation so far. One of the rare "markdown" tools that actually save your content to markdown files and not to a database with the ability to export to markdown. It also has a cool feature built in where it indexes all of your notes/tasks/paragraphs and lets you build queries around them sort of like the dataview plugin for obsidian.
• Emacs: I haven't seen emacs mentioned yet, but emacs+org-mode is still great. The mobile apps just don't live up to the desktop experience, and you'd still have to figure out how to sync your notes yourself. Logseq's outliner format is a similar feel afaict

I use obsidian with obsidian-livesync for selfhosting the notes. Works pretty well across linux, macos, ios so far

Logseq actually does not need to be run in a browser, there are apps for every system. It does not have any sync server to host though (so far) so you have to use syncthing or something to have your notes available between devices. It does store notes in .md format with clearly labelled names so you always have access to them.

It does have a learning curve and android apps still do have some bugs to iron out, but I started to really like it and use it as my bullet journal.

The whole system of linking notes and even singular text blocks works really well in my mind. I can write a quick note about my health in today's journal file and tag it with #health and when I go to the health file it shows every mention of that tag from everywhere.

For the past many years I've simply synced my notes across devices (originally from webDAV, currently Syncthing) and open them with my favourite Markdown editor for each platform. On my android phone it's Markor, and Marktext on desktop.

I've tried so many note taking apps but especially Joplin's weird renaming of my files cooled my enthusiasm for One App To Rule Them All. I do understand the attraction of it, I just prefer a simple setup where I'm not bound by any developer (team)’s whims.

Honestly I just have a directory with markdown files I sync between my devices using syncthing.

For editing on pc I use neovim and for editing on phone I use markor.

https://noteapps.info

Obsidian is my favorite thus far. It sucks at checklists/Todo though. So I use Quillpad as a shopping list keeper and Tasks.org as my task management/Todo, both syncing to my self hosted Nextcloud instance.

I'm still on Obsidian Sync because I couldn't get Syncthing to work reliably, but that was very early in my selfhosting journey, so I will try again.

Nextcloud notes. They'll sync as text filed between your devices. You can use markdown, and they have a mobile app.

Dokuwiki with markdown plugin, or gollum wiki (or one of its forks) should meet the requirements

Lots of good suggestions. I've also used memos, but wasn't a huge fan of how the notes were organized. Solid app and definitely worth a look.

https://github.com/usememos/memos

Edit: I'm holding out hope for when notesnook goes self-hosted.

Edit 2: after looking at my older instance I see they save the notes in a database and is not relevant to your question.

The closest one I've found to what I'm looking for in a note taking app is Obsidian. Really it kind of set the standard of what I need with how efficient it is to use. The only issue is syncing to my phone and tablet. I'm using Nextcloud and so far have only been able to get "read" access on my mobile devices. If I try to create/edit a note it gives me access errors that I haven't found a way around. This isn't a huge problem because I mostly reference notes on the devices anyway and am not making changes to them. Mobile note taking is typically done in my physical pocket notebook anyway.

Yes Joplin encrypts the notes.

Obsidian + private GitHub repo hosting

Privat gitea server.

Silverbullet but you have to do your own authentication and TLS

It's not exactly what I think you're looking for, but depending on what you are trying to do, maybe look at hackmd/codimd.

It's more like Google docs meets markdown formatting. It's goal is realtime collaboration but I've definitely used it for syncing todo lists with people.

Codimd is the self hostable version.

Oh, and I think there is a way to have it sync with a GitHub repo too, in case that is useful.

Links for convenience:

https://hackmd.io/#

https://github.com/hackmdio/codimd

Try Orgzly with Emacs Orgmode

Obsidian without a doubt!

Maybe you should try Anytype. It's Open Source, encrypted, has applications for major OSes, provides synchronization, allows export of documents to Markdown and PDF. Sometimes it's rough on the edges, but I think it has a potential.

Another vote for Obsidian. I use it with the remotely-save plugin via WebDav and Nextcloud - completely self-hosted, I haven’t even made an Obsidian account. Sync conflicts are very rare, I’m using it on iOS and four desktops. While I wish it was OSS, nothing I’ve looked at even comes close to the flexibility of Obsidian. I’m using it for daily notes, habit tracking, task lists, and most recently to write a book.

Check out SiYuan. It's an open source, self hostabole version of Obsidian.

It uses a database on the backend but editing is done in Markdown and it can import / export Markdown files.