I've always viewed it as the EMCEE.  He is the one who starts the whole thing - and ends it - and is the one that's sort of "in charge" of everything that goes on, onstage.  It's almost as if he is the story teller - the narrator if you will, and the whole show is somewhat of a morbid fantasy that he controls.  That might be a bit too cosmic but that's always been my strongest assumption seeing this show and having done it twice (Herr Schultz).  Sally and Clifford are on equal ground more or less but really secondary to the Emcee in my opinion.  I guess it would vary with any individual director who saw it differently of course.