This is awfully low-tech and I hope I'm not totally wasting your time, but I was thinking about ways to add footnotes to LJ and came up with a crude solution involving backdating and target windows:
Someone clever could probably easily make a client that automates this with two update windows: one for the main entry, another to type in footnotes and post them automatically backdated. A button could be added to insert links into the main, and voila: an LJ updating solution that allows for fairly robust footnotes with no changes to the LJ infrastructure.
I'd love to hear if there's something to do this already, or improvements on this jerry-rigged system. An LJ with easy footnotes would make a lot of academics happy!