I'm with Saxon and a few others on this. While I'm sure you could find a program to emulate an environment in which binary will work and run as if it were a separate cmd line program there would be no purpose other than novelty. If you want to program something that will actually work and be useful use a tool like C++, VB, or Java and their compiling languages / packages.
There would be no way within todays environments to create a program that would really do anything. If you could it would take freaking forever to code it in binary.
I agree it would be kind of neat, but personally I would just go and write something that you could use and would be functional in VB or C++. And it doesn't have to be something huge and corporate, you could program something to keep track of your budget, grades, and a multitude of other things that would make every day life a little easier.