1. Beat Classic Mode on Hard with Link or Zelda
2. Complete 200 Vs. Battles
3. Get Ganondorf to join your party in Subspace Emissary
Ganondorf is the chief villain of the beloved Zelda series. Naturally, only the heroes can unlock him. You must clear classic mode on the Hard difficulty with either Link or Zelda in order to battle him. Be sure to stock up on a lot of coins if you plan to attempt this. It will cost you 50 coins per continue, so I would recommend having 2-3 hundred coins and a good skill level with Zelda or Link. You could always go for the 200 Vs. Battles option, but as usual this will take a lot of battling. You can also unlock him without a fight if you can get him to join your party in Subspace Emissary. To do this, you have to save Link and Zelda near the end of the game. Ganondorf will appear after you complete the stage.
Once he challenges you, Ganondorf can be easily outmaneuvered. He is extremely powerful, but also very slow. He is also completely lacking in projectiles. This means he's an easy kill if you run away and throw things at him. Just don't let him get a hit on you. He can trash you very quickly if you let your guard down. Dodging and running are your best bets on finishing him off and unlocking him.
Every man dies, but few truly live. Live your life to its fullest, every day as if it were your last.