I'm having trouble articulating my thoughts, but my vote is with Wind Waker. Maybe not strictly as their best story, but for me, definitely Nintendo's best storytelling. Or something to that effect. And I think that's just as important.
When I first played the game, Nintendo managed to fill me with a sense of adventure and whimsy that I'd never before experienced. The game's component pieces all come together to really fill out the world they built. The characters were full of personality and charm. The dialog was excellent. The artstyle, while at the time was largely chided for being too childish, was spectacular. And I know Nintendo gets a lot of flak for not stepping into the voice acting age, but I really enjoy the personality miming adds to their characters. I think it's an approach that is very hard to change, since it affects the tone of the delivery so much. I think Square-Enix and the FF series are experiencing those growing pains, as I believe that a lot of what people hate so much about their games now, were prevalent in their earlier games. I think shifting to full voice acting requires a shift in how dialog is written and how characters are animated.
Anyway, that was a tangent. I really enjoyed how Nintendo humanized Ganondorf, even just a little bit. That ending sequence was so well done, as to be unforgettable for me.