I'm surprised that Joplin hasn't really been mentioned here.

It supports hierarchical or tag based notes + to-do lists, in plaintext/markdown/wysiwyg. It supports syncing to several providers, and I sync with my personal webdav server. It has vi/emacs keybindings and supports external editors. It also has a mobile app.

So I use that for digital notes, and a nice leuchtterm grid journal for physical notes. I generally do language studies in the physical journal and use the digital notes more for references.