Well the number one thing you need is practice and experience. A lot of it. Just like you do with anything, especially artwise. Take a look at good examples of pixel art and see what they do with it, analyse it for yourself. Though I don't recommend it in terms of producing and submitting art in the long run, editing existing pixelart for study purposes is a good idea.
As for the program used, I suggest GraphicsGale. It is the bestest.