The best Zelda game is the one that you love the most.
The best Zelda game is the one that you can live comfortably inside. No two Zeldas are identical.
To celebrate the release of Wind Waker HD—and A Link Between Worlds later this year, one supposes—we present our five-part head-to-head comparison. We will be condoning violence, daring to apply decades of Zelda experience to make a final judgment on which is the Best Zelda Game. This will be a bloodbath as much as it will be a celebration. There will always be ambiguity and personal preference, that is a strength that an individual always possesses, and it is good to have strength, and to express it when it is important to understand why one feels that strength has been earned. In this case, strength in knowledge about what makes these games, their stories, their messages—intended, or otherwise—relevant to a modern conversation.
These are the important ones to us. Objectively, they are the best games in the series. In them, we see ourselves. We see ourselves as brave explorers getting lost in the mountains, or in dreams, or trapped in vulnerable, cursed, wooden bodies, and then we engage that fear, just as Link does, reaching out arms to become stronger for it. Zelda games are good like that, fearless. Find a solution. Find an answer. Find courage. Refuse to be outsmarted. There's always a way.
This discussion begins in the center. It will work outwards from there. The obvious place to start is with Ocarina of Time, A Link to the Past, and Twilight Princess. They are cut from the same cloth. They all concern altered-states for Link, they all strive for a Kingdom-wide threat, they are the grandest adventures. These are main-line Zelda games.
The stories are similar in these three. They are exemplary of the Zelda mono-myth.
There was once a kingdom full of knights and horses, and there was a forest full of magic, and a royal family that was loved, most of all a very important princess, Zelda, named for her ancestors. There was a boy with a sword in his left hand, coming from humble beginnings, that fought a piggish beast to recover a golden magic that human hands struggle to fully grasp. The golden magic could be used to create, rather than destroy, if it could be respected.
These three games are the big ones. Each lives in another's shadow. It's the plotting for the story that makes them different and makes one superior to the others.