I have a set of binary configuration files with three versions each -- an original, and two differently-modified versions of each file. I need to be able to see the differences
You could have a look to ECMerge (a tool I work on), it has a 2 and 3-way diff of binary files (HEX + ASCII). There is no merge feature. You can move from changed area to change area easily and compact long zones (long insertions, changes or unchanged).