See Identifying identical files in my diffultils feature request.
I propose to incorporate the similar feature also into jDiff.
I could show a list of sublists to which the "different" relation splits a set of buffers (either the set of all opened buffers or also (on user option) the list of a choosen subset of all buffers). It should be easy to show the dual diff for every two buffers in the entire set of compared buffers: show the set of partions of the set of all compared buffers and make it easy to choose of them two for comparison.
Also please make it work together with https://sourceforge.net/p/jedit/plugin-feature-requests/383/
I think this would be better done in the PMD/CPD plugin. CPD is the Copy/Paste Detector that is part of PMD and does a good job of finding duplicate code across files and directories. It would probably be a somewhat small change to the CPD display code to show duplicate code side-by-side similar to JDiff, but without the diffing tools.