Phantom Ganon are Ganondorf's mysterious puppets who appear in four The Legend of Zelda games: Ocarina of Time, The Wind Waker, Four Swords Adventures, and Twilight Princess.
Ocarina of Time
The 1st Phantom Ganon is the boss of the Forest Temple. As Link enters the boss's room, he sees many identical paintings on the wall of a road leading to a dark castle; Phantom Ganon jumps into one of them with his horse. After disappearing, two Phantom Ganons ride to the front of the painting, and a purple hole appears in one of them, which is the one the real Phantom Ganon will jump out of. As he jumps out, Link's got to shoot him with an arrow from the Fairy Bow. After taking sufficient damage, he will leave his horse.
He will now start to attack by shooting an energy star at Link. He, in turn, has to bounce the star back at him with the Master Sword. He will retaliate but Link must not give up; after enough times, Phantom Ganon will eventually be hit and fall to the ground, paralyzed. The hero now has to slice at him with the Master Sword. After enough hits, he will be defeated. Link then gains a Heart Container and the Forest Medallion. As for Phantom Ganon, Ganondorf banishes him to the area between dimensions.
The Child Timeline's 1st Phantom Ganon, but 2nd Phantom Ganon fought by the Link of the child timeline is summoned by Ganondorf to aid him in his horseback battle with Link. After Ganondorf is knocked off his horse, the Phantom Ganons disappear.
Four Swords Adventures
The Child Timeline's 2nd Phantom Ganon, but 3rd Phantom Ganon fought by the Link of the child timeline is created by Ganon as one of his minions. Phantom Ganon confirnts Link twice, first early in the game, and again in the Temple of Darkness.
The Wind Waker
After withdrawing the Master Sword from its pedestal, Link travels back to the Forsaken Fortress to confront Ganondorf. Upon arrival, however, his path is blocked by The 2nd Phantom Ganon of the Adult Timeline. After a battle of Dead Man's Volley, Link defeats him and a Treasure Chest containing the Skull Hammer appears.
Later, after restoring the Triforce of Courage, Link traverses to the submerged Ganon's Tower, where he is again confronted by Phantom Ganon. This time, however, Link must fight him several times in a large maze with many doors. After each defeat, Phantom Ganon drops his sword. By going through the door that the hilt of the sword points at, Link is eventually rewarded with the Light Arrows. After traveling to the next room, Link is confronted a final time and defeats him solely with the use of his new Light Arrows.
Phantom Ganon was never created in the timeline, they have a counterpart named Agahnim who takes their place as Ganon's clone.