Joplin is pretty good for organizing notes.

Proton just bought Standard Notes, so keep an eye out for changes there. Otherwise, I use Obsidian but I have it sync to my home server so I can access the same data from my phone and computer.

Obsidian is pretty good, it shouldn’t collect any data by default. But you can also check out Logseq, an open source Obsidian alternative.

As they are closed source no one can tell you their true privacy policy. It seems better than average from what I’ve read but you never know…

Personally I use logseq and sync the files via a Nextcloud instance. I can only recommend it, although I also recommend spending an hour to learn the tagging and linking logic and reading through their guide on what’s possible. I still only leverage a minor part of the potential myself.

One that is closer to onenote (I think, never used onenote) is Joplin.

I use Obsidian, which is quite powerful with their vast plugin library. You can do a lot of automation, and you can check out some of Nicole van der Hoeven’s videos, who among other things use it to keep track of TTRPG campaigns, both as a player and as a game master. For example this one.

I don’t use their sync service, but have all files locally on my Nextcloud server. I sync them to my phone with Syncthing, which unfortunately means I cannot encrypt them with Cryptomator like I planned, but if you only use it on your computer, that is also something you could do. If you are paranoid about them still phoning home with your data, then you can block its network access with a firewall. I think you can install plugins manually.

I would have preferred it if it was FOSS. I have considered checking out Logseq as an alternative. But the bullet-based workflow doesn’t appeal to me, so I haven’t tried yet. I switched over from Standard Notes, and honestly it was pain to transfer because the text export from Standard Notes was all over the place, as I had used a lot of different note types. I tried to parse some of these smart notes they have, but I couldn’t quickly figure out how they were structured to automate it, so I ended up manually going through and copying over what I wanted to keep. I like the approach of keeping plain text markdown files. It is easier to export to another application in the future, although some of the content will be useless as it is explicitly written for the plugins (e.g. Dataview).

Since you’re specifically looking to replace OneNote, you might want to take a look at BookStack. It has similar organizational concepts, and I think it’s FOSS.

Logseq or Orgzly Revived

I use logseq for work notes and Obsidian for personal. Obsidian is more markdown which I like for my loose notes. logseq, on the other hand, is more focused on productivity and it’s fully opensource. Obsidian is only free for personal use, however their notes being closer to standart markdown means that they could be openned with any text editor and be just as functional.

Syncing between computers is easy – it’s just a git repo. Dealing with mobile is tricier but I never needed it so can’t comment much.

How about Notesnook? https://notesnook.com

Open source and end to end encrypted

I had almost the same question. So let me quickly share what I came up with.

I have a ton of notes in different areas. By I was not happy with the way Obsidian worked – synchronization specifically. I didn’t want to pay for it. So I got on a quest for the perfect note-taking system. It had to be:

• Markdown-first. Because we all know why;
• Interoperable. That is as few additional flavors and things added as possible;
• Portable. Such that I could open my Notes folder in any app;
• Synchronization. With as few additional crutches as possible.

Main text editor

Desktop. I use !helix@programming.dev. It has marksman LSP (meaning markdown support out of the box). This is how I know no other app is involved into writing process (no telemetry, etc). Also zero task switching this way. I still use !obsidianmd@lemmy.world from time to time. I don’t use Logseq because it has opinionated file structure, which doesn’t meet my interoperability need. Also, I don’t always need an outliner. You can turn this feature on in Obsidian, but you can’t turn it off in Logseq.

Mobile. I use the simplest markdown-capable apps for iOS and Android. Also, don’t forget Cryptomator.

Sync. For the most part I use !syncthing@lemmy.ml to sync all the notes. Such that they are not uploaded into any cloud storage. I don’t use iCloud, or rather almost never use it.

As for your question. Obsidian is a pretty good choice because of its extensibility, portability, and interface. Although it easy to get lost in the plugin rabbit hole. Its desktop and mobile (if you go for it) privacy policy is pretty solid. Client-first markdown app – nothing more and nothing else.

Lastly, there is this idea that one needs to sync notes via some cloud. Not true. You should consider your threat model first. Cloud sync is not must. In some cases, Syncthing is more than enough, is more private, and might be a more secure option (as it reduces your surface of attack to some extent).

I guess that’s all

Anytype

You can read Obsidian’s privacy policy. Basically, everything remains on your device unless you pay to use the Obsidian Sync. I switched from Standard Notes to Obsidian last year and I haven’t looked back ever since. You can use Syncthing to synchronize your Obsidian Vault across multiple devices. All you need to do is add the Vault directory to Syncthing, that means you need to first make a dedicated folder in your filesystem for the Obsidian Vault which you will be required to do anyway while setting up Obsidian.

OrgNote. The project is still quite raw but the developer works hard and the overall idea and philosophy behind the project is perfect for me. Fully compatible with emacs org-roam, most probably compatible with logseq. There is a “fully managed” free version with PGP support or an option for a self-hosted server.

Project: https://github.com/Artawower/orgnote Manifesto: https://github.com/Artawower/orgnote/wiki#manifesto

Obsidian and logseq

Nextcloud notes if you have a Nextcloud instance