This is a simple command line application that calculates the MD5 hash of a file. It can also take another MD5 hash and check whether they match. Run the program in a command line with no arguments (or --help) for usage instructions.
This is a .NET 3.5 program, and thus requires the .NET Framework 3.5. I have not tested it in Mono, but it uses no Windows specific functions, so it should work on Linux as well.