Earlier quoted context omitted.
You can try out brainstorm: github.com/Azeirah/brainstorm, Tags can be used to semantically link notes, or if you want to link to another note, you can just use []() markdown link syntax, each note has its own url. You can try the demo at sandstorm.io (install brainstorm as an app) Or you can try a slightly older version here: http://brainstorm-notes.meteor.com/board/Home Is that similar to what you're looking for?
Looks pretty cool, but I had trouble getting the links to work just using a note title. I'm also looking for something native that will operate on a folder full of text files (for easy backup, syncing, and versioning).
Someday I'll build the perfect note-taking application, quote me on that!