Vim has a built-in diff tool that can compare any number of files. It also works on Windows. You can find it at http://vim.org .
The standard vim installation for windows includes xxd, which allows you to see binaries as text:
So, for example, if you try:
xxd xxd.exe
You'll get:
0000000: 4d5a 9000 0300 0000 0400 0000 ffff 0000 MZ..............
0000010: b800 0000 0000 0000 4000 0000 0000 0000 ........@.......
0000020: 0000 0000 0000 0000 0000 0000 0000 0000 ................
0000030: 0000 0000 0000 0000 0000 0000 d800 0000 ................
0000040: 0e1f ba0e 00b4 09cd 21b8 014c cd21 5468 ........!..L.!Th
0000050: 6973 2070 726f 6772 616d 2063 616e 6e6f is program canno
0000060: 7420 6265 2072 756e 2069 6e20 444f 5320 t be run in DOS
0000070: 6d6f 6465 2e0d 0d0a 2400 0000 0000 0000 mode....$.......
0000080: 6ba7 bec3 2fc6 d090 2fc6 d090 2fc6 d090 k.../.../.../...
etc...
Thus, you can use xxdto upload your binary files to text files:
xxd orig > orig.txt
xxd mod1 > mod1.txt
xxd mod2 > mod2.txt
vim diff:
vim -d orig mod1 mod2
- :

( , 3-way diff VIM)
Windows, .
Edit:
xxd xxd -r:
xxd -r merged_xxd_file merged_binary_file
xxd manpage