I have to say Ocarina of Time....I'm not saying this be cliche but I believe it's the best fight because of the atmosphere. When you defeat ganondorf for the first time and think you've beaten the game, he reappears becoming Ganon, the King of Evil.
This is when that feeling of dread kicks in and you feel hopeless since you don't really know what to do the first time. The darkness, lightning, creepy-hopeless music, as well as only seeing Ganons bright, evil eyes really sets the tone for one of the most unique final battles in the Zelda series.
I've beaten the game about three times now, but when that final battle comes I honestly feel scared and hopeless, thinking to myself "How on earth do I beat this monster". In Ocarina of Time, it is way different then any of the other Ganon battles, because for the rest of them you go in confident in your skills and battle it out. You feel that way when you fight Ganondorf in Ocarina of Time but when Ganon awakes it's a whole new ball game. For a final boss to make me feel the way I do when i play is unreal. I have never felt that scared and hopeless when playing a video game before.
So I say that Ocarina of Time takes the cake as the best ganon fight because the developers really "linked" the player with Link.
