I've given up with trying to find The One True Note Taking Tool, so have ended up writing my own thing that I tinker with now and again to tune it to exactly what I need. It's essentially a simple web server that sits on top of a bunch of markdown files. The frontend renders the markdown using markdown-it and supports KaTeX for simple inline mathy things, along with the extended markdown stuff like tables etc. I've e…
Some nice features I've added over the years: bookmarklet and automatic page-screenshotting, tags (and smart auto-tagging), everything markdown supports, file upload and attach, media embed (YouTube link becomes player, eg). Oh, I can also attach email reminders and make to-do lists (with little checkboxes and everything). It started out very simple and has grown over time. Sqlite is a great foundation for projects like this. Strongly recommend.