This is no easy question, but an important one, so this is where I'll keep notes on what has worked for me.
A quick search with google gave me only two promising leads:
I figured I must be able to do better than that! But Sourceforge and Freshmeat gave me nothing better. I guess the good tools are buried inside the commercial software. But the software I use (Gramps) does not yet have the ability to compare two genealogies, so I press on.
Eventually I found a copy of each program that I could actually download (found GEDCOM Analyser eventually), they're obviously not maintained any more. I'll add a note about how I get on later.