ASCII vs BINARY checksums
Windows MD5 Sum generator.

MD5 checksums can be generated in 2 ways, ASCII and BINARY.
BINARY mode simply processes the file "as-is" but ASCII mode translates End Of Line (EOL) to the local standard before processing. For example, Unix uses CR (carriage return) as it's EOL character, but MS-DOS and Windows use CR-LF (carriage return then line feed)
In Unix the two modes produce the same result because no translation occurs. Under windows, I'm sure you can see that the results would be quite different.

The GNU md5sum defaults to ASCII mode and BINARY mode must be specified with the -b switch.