Not a huge one, but it is only free for personal and non-profit use. “If your notes contain content directly related to work projects or processes for a greater-than-one-person company, then you require a commercial license.”
Since it is on flathub and they don’t really nag you, I am sure there are people who aren’t really aware.
Seconding Obsidian - it's not FOSS, but the files are just markdown, nothing special, so you're not locked in. Self hosting is real easy, you just have to Sync the files, and everything follows. I use syncthing between my laptop and phone and am having a good time with it.
Whoops, should have noticed your endorsement of syncthing before posting a comment mentioning this.
While Obsidian does save to individual files, the Markdown they use seems to be a superset of everyday Markdown. Eg, being able to use callouts (eg, Note, Warning, Info, etc) and embedded linking of notes.
The automatic backlinks are fantastic. And I've discovered that if I rename a note, all links to that note get updated as well. So no need to worry about orphaning pages.
I've added a handful of plugins as well. Off the top of my head, one is a dynamic table of contents (for that page), another helps to compose/edit Markdown tables.