Having started with Joplin, the three things that took me away were the (at the time) lacking mobile support, periodic syncing collisions, and probably most importantly, their non-standard file format. There was a tool that could extract files into standard markdown format, then repack them, but the overhead was tiring, and meant a few key environments lacked access, namely when I was accessing a server from the rack, and when the mobile app acted up.
I actually moved to just using vimwiki style setup with markdown and a markdown editor app on my phone for several years, before I stumbled across Obsidian.
I've since been using obsidian for about 9 months now, which is longer than my time with Joplin, and I will say that, once I got a stable sync going (I'm using the simple sync plugin and my own s3 compatible server), the plugin support, decent mobile app, and native markdown files have won me over. Though I'm still eyeing open source options with Logseq, just waiting on their mobile app to pick up and properly support plugins. I'll be more than happy to port everything as soon as it supports that.
As an additional note, I will add that despite Obsidian being closed-source, I actually feel more comfortable with my data there than with Joplin, primarily because all my data is just common markdown. With Joplin, if I archive content, I have no guarantee the notes on the file format will exist in 10 years (they probably will, but it's still a real possibility). With Obsidian, it's plaintext. There's nothing to need to rediscover, no file format to decode, just good old plain-text. In 40 years I'll still be able to read those files (though the storage media is a very different story). Sure Obsidian can change plans mid-stream, and I don't trust they wont, but all I gotta do is go back to my markdown editor and vim. No sweat.
> In 40 years I'll still be able to read those files (though the storage media is a very different story)
With Joplin, you can easily archive as Markdown+FrontMatter and that format will still be readable 40 years from now with text and metadata included.
Additionally, in case you forgot to make a backup, and 40 years later all traces of Joplin have disappeared from earth and you can't find an old version of the app, the backend is a simple SQLite database, so you can do `SELECT * FROM notes` and get your content back.
> Though I'm still eyeing open source options with Logseq, just waiting on their mobile app to pick up and properly support plugins. I'll be more than happy to port everything as soon as it supports that.
I tried it out for a while, I'm sure that it's a great program and it's various free sync options & encryption system may immediately put it ahead, but as a basic user I found it much more complicated to the point where I couldn't figure out how to simply sort files into folders (and I don't know if that's something you can do). There's an interesting tagging system to search posts with and there's a ton of plugins out there if you want to do things you can usually do.
I really ought to give it a shot again when I've got a clear head.
If you want a FOSS alternative to Obsidian that's just as simple you could try Zettlr, but currently it's rather rough. You have to change the UI settings to get the folders/file view that Obsidian has, and I found readability to be rather poor. Initially there's no way to make in text larger without zooming in the entire UI, font, and the themes that are available aren't the best for writing or reading notes (and if you like one specific theme you're sod out of luck if you want a darker version of it) – if you want to change things to your liking you have to experiment with the experimental Custom CSS option.
Tried both for quite some time, Obsidian has better community plugin support, better sync (paid) and stores plain text files instead of using a DB. Most importantly the mobile app (at least for iOS) of Obsidian is 1:1 with the desktop app.
Switched from Joplin to Obsidian and haven't looked back. Both apps are great initiatives though!
Does it reflect notebooks/folder structure also in the filesystem? That's exactly what I need from a PKM tool: that not only the files but also the structure of the notebooks is reflected in the filesystem so I can have interoperability. This way I can decide to work with Obsidian, EagleFiler, Notebooks.app or DEVONthink while also having the possiblity of using the regular Finder to work with my files.
For me personally the only upside is that I don't have to pay separately for syncing the documents and can use Dropbox instead. Yeah I could use Dropbox on my phone too for obsidian but it's not a great experience when all you want is taking/reading notes without hassle.
Worse. I want to see the result when writing so I always had to have a separate preview window open which stole a lot of screen space. Obsidian solved this with the WYSIWYG mode where a paragraph transforms to markdown when you click on it, but the rest of the document shows the end result. It makes the experience a lot nicer when embedding tables and images that you can look at directly and write in-depth about without just seeing a filename.
