I think it would be very nice to have a plugin for comparing executable files. Under linux the ELF excutable file format contains sections that are used by the dynamic loading. The plugin must ignore those sections in order to be able to say if the file is the same or not.

http://www.cs.ucdavis.edu/~haungs/paper/node10.html contains full information about ELF file format. The plugin should be able to consider the "dynamic linking sections" as unimportant.