This is the official page of the free program CubeDiff. It is a simple Perl script, and I am not a Perl expert, so don't expect much from it.
Since CubeDiff is free software, you can download, use, modify and redistribute it to your heart's content, with some caveats (see license). If you would like to share your corrections/additions with me, I'd gladly hear of them by e-mail.
CubeDiff takes two or more valid GAUSSIAN-type .cube files, along with instructions to either add or subtract each one to a total, then outputs that total to the standard output (the screen). The output result is in turn a valid .cube file, that can be read with, e.g., Molekel.