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.
I didn’t mention it, but that’s actually my one (small) gripe with Joplin. It would be neat if I could access my notes with any markdown editor without having to open it through Joplin. That said, I don’t know how I would’ve handled the file structure differently while keeping features like the history alive.