TKDiff used to (3.x versions) allow you to specify multiple file pairs on the command line:
Imagine I've got the original in directory 'orig' and the modified in directory 'new':
tkdiff orig/file1.txt new/file1.txt : orig/file2.txt new/file2.txt : orig/file3.txt new/file3.txt
That would bring up tkdiff with the diffs for file1, file2, and file3 all together -- the "File Pairs" menu would list them as follows:
orig/file1.txt -- new/file1.txt
orig/file2.txt -- new/file2.txt
orig/file3.txt -- new/file3.txt
This doesn't work any more.