od -c myfile.pub). Then there are three columns for each file: Hex, Decimal, and (if printable) the ASCII character. If 1.pub's value is higher than 2.pub's value, then the row is light blue, otherwise it's yellow.
New tools: getdiffs.c is a hacked version of phtml.c. The latter, phtml, does a simple binary "diff" of the files, as described above. It also includes the common text, which is marked in white. The former, getdiffs, only shows the differences, but does mark the areas of commonality by a simple horizontal rule, so you can see which chunks go together. They also both have a "skipA()" and "skipB()" function, which allows you to mark places in the binaries where you can see that one includes a longer entry than the other. So, where one file stores its own filename as "C:\x.pub", and the other stores it as "C:\somedir\y.pub", you can blank out the "omedir", to leave a single difference, of "x.pub" vs "s.pub". This is because binary diff is very difficult to automate; text-based diffs know that an end-of-line is a significant character, and can therefore spot related lines. With a binary file, you've just got a load of ones and zeroes (which I'm lazily interpreting as bytes). If you don't deal with these differences, you won't spot later commonalities.