Anytime Ganondorf (or any of his phantoms/possessed Zeldas) heaves an orb of magic at Link, Link can deflect it back by swinging an Empty Bottle at it. When fighting Agahnim, Link can use the Bug-Catching Net to swing the magic orb back at the evil wizard. (You still have to watch out for those fake blue-beaded magical attacks though, those will still hurt you when struck.)