If you have a commit that exists on two branches, in gitk you can mark one, then select the other and choose to compare the two. This results in a diff of the two diffs, rather than a diff between the two trees, which include many other changes that have nothing to do with either commit.
Is there a way to do this on the command line? I thought it would be git diff -c or --cc, but it doesn't seem to filter out all of the other differences between the branches.