Selfhosted

I write nearly everything in markdown. Like you, I don't want databases, or other barriers that will complicate portability.

I just use my text editor of choice, usually VSCodium or vim on the desktop, and Syncthing to keep the notes synced across all of our devices.

On Android, I've been happily using the Markor markdown editor for years. I've tried several others but always return to its simplicity.

All of the above editors support opening folders in a tree view, so you can easily keep your notes sorted under a traditional folder structure and find what you when you need it.

Edit: Forgot to mention that Markor does have a dedicated to-do feature too, which also uses markdown.

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

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.

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 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.

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

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 without a doubt!

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

https://noteapps.info

Obsidian + obsidian git plugin