Hmmm, well, I would have to choose the Master Sword. Mainly, I like being able to use a shield whenever I'm not attacking, plus, in LttP, it can shoot Beams. ^_^

However, the Biggoron sword is also really useful. I like to use it against Ganon in the Tower, reflecting back his power back with the Master Sword, than switching to the Biggoron for the actual physical attack.