Logseq. It works with Markdown or Org. Joplin is fine but I've moved away from it for Orgzly Revived + Logseq mobile/Emacs Orgmode + Logseq desktop all integrated with each other to do some stuff Logseq and Orgzly cannot do alone.

You will not find a better option honestly I love my tools. Tried a lot of things and this is one that will grow with you and never overwhelm you if you respect it.

Particularly nice to be able to smoothly turn Logseq/Orgmode stuff into LaTeX stuff and use Emacs Zotero integrations. I can publish professional-level papers and articles of pretty much any kind, from the same system where I work on Minecraft mods and remind myself to do house chores so my wife thinks I am a genius (because I am). I could write an entire textbook with it. It feels like being forced to use a revolver for years, and then switching to an AR platform.

I've been using Zettle Notes with syncthing for a few years now. It syncs with my laptop as just a directory of markdown files that I also edit with Vim (plenty of good plugins like Vim wiki).

I've never used it, but I've heard good things about Notesnook.

Joplin. I use it on my phone, multiple laptops and Linux desktops.

Currently using siyuan. Just wish you could use the app with a self hosted instance.

Actually, you can use Signal for this, if you have it on both your phone and laptop, and use "note to self." I prefer this because it's very straightforward and isn't bogged down with a lot of extraneous extra features that other notetaking apps I've tried tend to have.

https://silverbullet.md/

It's like obsidian (I hear) but FOSS. I love it and it's by far the self hosted service I use most.

It stores your notes in a plain directory hierarchy of markdown files so you can just point a cron shell script at it to git add/commit/push at your desired internal and you've got history tracking/backups too

Edit: also provides a PWA so you can "install" it on your phone instead of always using a full browser.

Edit x2: includes a Lua interpreter so you can get scripty with it. I use that functionality more than I expected and I suck at Lua

Edit x3: and it auto synchs to each device when open with conflict detection. Full copy is stored local to each device, synched when possible

I'm using Logseq and it's the least bad of the FOSS options I tried so far.

obsidian is not FOSS BTW

I’ve been using a self-hosted Jotty instance, it’s been pretty great!

https://jotty.page/

Joplin can sync between phone and laptop with a number of network storage options

https://joplinapp.org/help/apps/sync/

or you can self-host Joplin server.

https://github.com/laurent22/joplin/blob/dev/packages/server/README.md

You can self host Anytype. It looks like notion, but is FOSS and total under your control.

notesnook

I use Joplin through some WebDAV with my cloud provider, kDrive.

Works perfectly once set up.

I don’t know if you could make it work directly from your phone to your computer though.

Is there something wrong with Standard Notes that I should be aware of? It hasn't been mentioned here. It has the AES-256 encryption standard, there is a free tier, it's open source and it undergoes regular security audits.

Obsidian + Syncthing has been working prefectly for several years now for me, across Windows, Android and Linux.

Could look into self hosting an Obsidian Sync server, see this blog:
https://pinggy.io/blog/self_hosting_obsidian/

Obsidian - https://obsidian.md/

edit: And you can obviously do it without pinggy's tunnel for remote access.

not (completely) open source but signal has a "note to self" function i use for that

Notesnook should do it! It has a premium monthly subscription thing that gives you some extra functionality, but the free version does sync automatically between devices. I've been using it for a year now myself and have had no complaints.

Anytype is nice.

I found the best option markdown on my pc and a notepad outside.

I've set up Joplin with Syncthing and it's been working for me.

Syncthing and Org Mode.

I am currently in the process of migrating my Google Keep notes over to a self hosted instance of La Suite Docs. It sounds like a big Google Docs alternative, but feels way more like a notes app.