Try Compare Suite, it's has a function that generate comparative report as for single files as for whole folders.
I'm using it in the following way - compare two documents (if they has a common ancestor), then generate comparative report and use some ideas or citing from it to write comparative analysis.
As for comparing absolutely different files, then it will not do a trick yet. But I've contacted AKS developers and they said that new release of Compare Suite will have a feature for my needs, it will be able to compare two documents by keywords, so I'll be able to learn what keywords are common and what are unique. I've tried this in Compare Suite ONLINE -- it's some on-line representation of future release and it seems to work as advertised.
Think that it's a good tool that can help in writing comparative analysis.
P.S. Compare Suite URL:
http://www.comparesuite.com
Let me know if I can help about ideas on writing comparative report.
Dennis,
dencaffer@hotmail.com