Currently I'm using Joplin with Syncthing-backed file system synchronization. I'm pretty pleased with it, as I do like tagging- and Markdown-based systems.
I plan to upgrade to server-based synchronization, but before doing that, however, I wanted to see what other people are using.
Edit: So far I see a slight favor towards Joplin and Logseq, but I totally didn't expect (and appreciate) getting so many different answers.
Logseq, it’s a lot like Obsidian as it also has knowledge graphs, tags, is markdown-based and self-hostable but, in contrast to Obsidian, it’s fully open source
Joplin. Obsidian is not open source, doesn’t have native self hosting and it gets complicated. Joplin is very simple and just works. Although, it stores the notes in a hashed database, so you can’t edit raw files without Joplin client
https://notion.so It's a web-based editor with a good android app. Has basic formatting, plugins/integrations, and dark mode. It's free for individual use cases. Has some nice paid features for collaboration and business use cases, though the free plan still allows sharing and concurrent editing.
E: noticed this is in self hosted after posting. Maybe not what you're looking for, but it's a good service if you're ok with that.
I've been running the Joplin server for over a year with clients on four laptops and three phones and share notes with my wife and its wonderful. There are certainly quirks and sometimes sync issues but by and large I'm really happy with it. There seems to be one cluster of notes I have that always irritates a fresh client sync and it shows up at 50 conflicts but I work through it. Also my notebooks are huge and the first sync can take an hour. It's a lot slower than I'd expect.
I used Joplin in the past, but just didn't quite get completely comfortable with it.
I also tried Nextcloud in the past... that project has become too big for my needs and the file syncing had issues.
Logseq is very similar to Joplin (ie markdown files), but IMHO the editor is easier with Logseq, plus the files are just simple plaintext files, named after the page title, so are easy to edit outside of the application (and immediately update in the app)
At first, I was a little unsure of Logseq's default of working as a daily journal, but after a while it makes more sense for me - I use it at work, so 99.9% of my notes are meetings, tasks that occur during daily life... and of course those daily journals can refer to other "non-time based" project pages...
I also use syncthing to sync the notes between android phone, linux and Windows laptops and my NAS... so that wouldn't change for you.
QOwnNotes (had to look up the exact name as it's the stupidest app name ever). but compared to joplin it's lighter, faster, simpler (no database but individual .md files and folders) and works well enough with syncthing.
I am currently on Obsidian without any sync at all. Using this in both desktop and mobile.
But used it more in mobile for an offline note-taking app where I could write and read them without any internet connection. Especially to load images from local, make categorization (folders) and more with data I had in my mobile.
While for desktop, I rarely opened it anymore. I am more into VIM with markdown format and then just push it to git host for a quicker note taking.
orgmode with neovim on PC and orgzly on phone. syncing with syncthing
Edit: I'm actually using orgzly revived, a community maintained version of orgzly, since orgzly is no longer mantained
For anyone who is interested in note taking in your everyday editor like vim or emacs, orgmode is an emacs tool (in neovim there is a clone plugin) for note taking, todos, agendas, etc. It uses a format similar to markdown, and a good part is that with the orgzly app you receive notifications for your events. So basically you can use orgmode as a calendar as well (I do!).
Joplin syncing on my Nextcloud instance. I love being able to quickly screenshot something on my laptop for reference and later retrieve it on my phone :)
I used to use Joplin, and its great, but the Electron client isn't great on Linux mobile, so now I am using GNOME Paper on all devices, synced via Nextcloud.
It's much simpler than Joplin but I need exactly 0 of the missng features.
Historically I've been using Google keep or one note (I'm a monster I know). I've been trying to see if I can migrate over to Nextcloud notes as I slowly de-FAANG my life.
I've tried lot of different apps, but I think I've settled on Trilium for now.
It doesn't have a great mobile experience, but the web app works fine on mobile. The app in general is super customizable and way easier to write scripts / plugins for.
I used to use Joplin, I liked that it integrated with my Nextcloud, and the markdown format. However, the way that it handles the markdown files was too black-boxey to me, with the way it split them up in a weird scheme.
Now I use Ghostwriter with straight markdown files inside my Nextcloud folder. So I still get the syncing functionality, but a more flexible setup that doesn't require a specific app to access all of my notes.
I find Joplin perfect for my needs. Markdown, embedding images, links etc. I sync to my selfhosted nextcloud.
I like tags, I would like them to add a "directory tree" type of view to help sort "folders" (the thing they call "notebooks") but only because I am more used to just filesystem type structured filing. But the notebooks and tagging idea works for me too.
I strictly use it for notes/note keeping, in particular "HOWTO's" and specific topic notes. So I dont even do a great deal of markdown in my notes, but I love the ability to add screen captures etc to them for clarity.
And being on nextcloud, I can access those notes anywhere on any device, PC, Android, Raspberry Pi!! Joplin has an app for all of them
Joplin uses it's own database so interoperability is not perfect. Markor is so effing cool. That's on Android. On the laptop I use want ever is best suited for the task. Most often, a vim variant of notepad++
Siyuan. Ive been using it for a while now and find it very effective for my needs. Its gone through quite a few updates since i started using it and became open source in that time. It even has an android version as well which i do have installed on my phone but admittingly rarely use. I prefer writing information on a keyboard generally.
For long-term, permanent notes, I'm using Obsidian with Nextcloud and FolderSync Pro (which I also use for backing up some Android stuff to my Nextcloud).
For quick, easy notes while on the go (or that I need quick access to while out and about), I use Memos, which is more of a Google Keep replacement.
I've been using Trilium Notes for the better part of two years and love it. I have used Obsidian and similar markdown apps, and I find it frustrating to add images due to the need to store them in a separate folder and reference them instead of just pasting them into the page and being done with it. To me, that's a barrier for notes when I'm trying to brainstorm. I really do like markdown, but it doesn't work with my though process.
I have a sync server setup at home (with no outside access) and do my main writing inside my network. For notes on the go I use the Notes app on my iphone (its quick and easy) and then drop the notes into Trilium when I get home.
Ghostwriter and syncthing. Ghostwriter really has a good focus mode that really gets me in the right spot for writing. I use Markor if I am on Android and syncthing still works there as well.
VSCodium on the desktop, and Markor on Android. I write everything in markdown, and VSCodium is already where I spend half my time editing and writing code, so it was an easy choice. I also use Vim for quick one-offs, especially if I'm already working on a project with it.
Like others here, I also use Syncthing to keep my notes synced between home server, remote clients, and mobile devices.
I use Vscode with markdown preview, with a git repo. The only downside is that Windows incessantly wants to group instances of an application, so it's hard to keep my notes separate from my coding stuff.
Trilium. Tried a bunch but fell in love with this one. Others either didn't have support for inline math or weren't wysiwyg (Joplin). Also easy syncing between computers with its own server in docker, and it even doubles as a web version of the app.
combined with some bash aliases, neovim config tweaks, and some bash scripts I've cobbled together over time. Then syncthing to share it across my laptop and desktop.
I've tried a few different note taking apps but I always find myself coming back to vimwiki. Its not the most feature rich 'app'. Matter of fact its pretty simplistic but I dont need or want most of the advanced features of other notetaking systems. But what it lacks in features, it makes up for by being a vim plugin. Seriously, I can't handle using non-neovim text editors/note taking apps. Having all of my neovim plugins, and other config tweaks make vimwiki the handsdown winner over the rest.
The missing vimwiki feature for me was a running "to do list" across all of my notes. So I wrote a script that got me the to-do list feature I needed.
I personally like Nextcloud notes for quick notes and nextcloud collectives for detailed stuff e.g revision. With nextcloud tables and deck it makes a great notion replacement
on a desktop or laptop I use Emacs org-mode. on my phone I have tried so many options and the best thing that I found for me is Delta chat. I just use the saved notes which is basically an email to myself.