Well it might be helpful to have every note point to a file, but I don't think that it's really useful. I think the more useful use case will be to create a note who's content is a file.

Now that I looked at the content of a tomboy note file this wont be useful for tomboy since they contain a lot more info. Maybe have it possible to specify backends for the notes. Default, File, Conboy, Builtin Notes, etc... Each backend will basically have a function to load a note, save a note, and list possible notes.

This is starting to sound like overkill though...