Noah,
As you know cause and effect is both important and will always occupy a major share of the attention, as I came to realize when I was in the masters history program at Vanderbilt before the law beckoned.
However, as a cursory review of LSU's Civil War Book Review or the university presses catalogues of the likes of LSU, University of North Carolina or Kansas show, there are many fertile areas for mining. One problem that I have is one avenue leads down to the next and there is just not enough time to explore everything. As soon as I finish what I'm reading (Don Fehrenbacher's book on Lincoln, Prelude to Greatness), I will be exploring Freehling's books on Secessionism and border state unionism, a fascinating topic.
Since both Tom and Mike mentioned their reading interests, mine is principally Lincoln.
Over time I would like to hear more about your program since my hope when I retire is to go back and get my masters in history (starting from scratch though )
Brad