Joplin stores its files inside a database. Obsidian stores all notes as individual plaintext Markdown files.

In the first instance, that's clearly more future-proof and robust - your notes are immediately available in any application without a layer of abstraction. You can't have a single file corrupt and destroy all your notes.

I vastly prefer it for that reason. I want to know these notes are still going to work fine in 10 years, and be easily accessible.

I use Joplin for a simple notes app mostly for my phone but I do have it on my desktop and sync. What I do not use it for is my desktop notes collection which is a several thousand notes pages some quite big. I use Zim for that. It is a desktop Wiki.

I do not use Obsidian but it seems like knowledge base and linking is what people rave about. These are the ways in which I use Zim for example.

Write 4000 notes

Get a new device

Sync

Die waiting

I do miss joplin, but not cuz it looked good or cuz it was good at syncing