Out of all the appearances by Ganon, his Ocarina of Time incarnation is my favorite. His story was a bit more fleshed out. The first time he took a humanoid form as well, dubbing the name Ganondorf. You first learn he's an claimed ally of the King of Hyrule, but Princess Zelda does not have the same trust as her royal dad.
As she was right as he quickly leads a rebellion, and tries to kidnap Zelda. He does a rather impressive feat of intimidation on Link (believing him to be a foolish boy who was trying to be brave), and departs. So you have to go into the future, and awake the remaining Sages who are capable of sealing Ganondorf away in the Sacred Realm.
I loved the scene where Link is aided by the sages by a magical bridge to enter Ganon's Castle. He must be pretty lucky to have the only castle that hovers in mid-air. Moats are for losers.
Then you get to play an impressive game of light-blast tennis with your swords. One of my favorites.
Then the epic one-on-one battle against his final Ganon form inside the giant ring of fire. Luckily I got the Biggoron Sword so I didn't have to stick to arrows while I waited for the Master Sword to be sent back to me.