lucy24 - 9:44 am on Jul 2, 2012 (gmt 0)
Any diff/merge program should do it. Unfortunately the best one I ever had, DocuComp, dated from 1991 and only ran on Mac Classic. You could feed it two entire novels and it would spit out the passages that one had swiped from the other. (I had great fun with this feature in an e-book, though I realize "fun" is not your goal here.)
What platform are you on? I've currently got something called DiffMerge but it isn't nearly as nice, especially on the large scale which is what you want.
Can you do command-line stuff? I know someone using Linux who might have something useful.