[yk]

For academics, you can pry Latex from their cold dead hands, so better include a Latex mode. Personally, I like emacs and I think that modes, aka the plug-in architecture has really a lot of merit, so try to expose as much as possible of the documents to a plug-in api. ( That one only becomes important when your project is very successful, but perhaps it is good thing to keep in mind.)

One thing I would like to see in emacs is something similar to scrivener's corkboard, basically a virtual corkboard were you can place index cards and group them together.

[fizzbucket]

Awesome; but what do you reckon the best way to implement a corkboard is when it's entirely possible that you're dealing with individual documents, not Scrivener's groups of them? (Sorry, that sounds snarky; it's a genuine question; one global corkboard, per folder, or what?)

[yk]

Sorry for the late answer, just seen your reply.

Again I am thinking about emacs, there you could have multiple cork boards, with multiple Windows. So basically, you open a cork board view, which in the background has a cork board buffer. And in principle you can then open a second cork board window to the same buffer, so that you can lock at two different places at once.

As for how to implement it, I am not sure, my crazy first idea would be as a clip board on steroids. So you mark some text and a index card with the text appears in the cork board.