This MD5 hashing tool, part of the GNU Coreutils suite, has been a standard in the computer forensics community for some time. It is intended for *nix systems, but has been ported to the Windows platform. It should be noted that the program has options to read files in "binary" or "text" mode, which can produce different hashes. The text mode is the default on most platforms, which is different from other hashing utilities such as md5deep.
To use this tool in binary mode on Linux systems you would use the command:
md5sum -b [filename|volume]
md5sum -b /dev/sda
md5sum -b file.dd