There are better/more friendly tools out there than Diff or FC. I use (for work stuff) a GNU-licensed piece of software called CSDIFF which will do this job well:
http://www.ComponentSoftware.com/csdiff
I haven't tried using mod files yet, but some issues occurred to me - how do you get around;
a) communication of a set of mod files? I mean, do you give them a name and distribute to all players for PBEM, who then point to them?
b) playing simultaneous games with different sets of files; do you have to go in and change the 'pointer' between taking turns?
c) trust! 8-) I mean, could one player make an outrageous change to a ship type (5000 space cruisers?), build a dozen of them then change it back? Would the other machines in the game detect this, accept his changes or collapse in a heap?
d) modified sets of graphics. If I want to use a 'MyBEMs' set, do I have to send this to all the players in a PBM game beforehand? If a player doesn't have the appropriate set or has mis-installed it, will the game use one of the 'default' sets of graphics?