Ganondorf

Ganondorf: Ocarina of Time
Every hundred years a man is born of the Gerudo Tribe and becomes the King of Thieves, this is that man. Ganondorf is a well accomplished man with evil intentions to learn the way of the Triforce. His swordsmanship skills are simply astonishing and he holds great power within him. Ganondorf has plotted to conquer Hyrule and become a powerful menace, he must be stopped. In The Legend of Zelda: Ocarina of time, this evil Gerudo leader has an ambition to rule Hyrule and bring darkness upon the land. When Link removes the Master Sword from the pedestral in the Temple of Time, Ganondorf sneaks into the Sacred Realm discretely and attempts to reap the Triforce. It is said in Hylian Lore that a pure heart will be able to take the triforce and use it for good, pure meaning good. It is also said that if a bad heart takes the triforce, the bad person will be able to use it in a horrible way that could devastate everything. Unfortunatly for Ganondorf, there was a corruption and the Triforce was split, this was most probably because Link was the rightful one to the triforce as he pulled the Master Sword out. The Triforce of power went to Ganon, but the other two; courage and wisdom went to two other people. Link received the Triforce of Courage and Princess Zelda received the Triforce of Wisdom.

For seven years, while Link was sleeping in the Sacred Realm, Ganondorf took over and ruled Hyrule, under the view of his dark eye in his horrible dark palace. This was mainly because of the Triforce of Power. However, Ganondorf could not fully conclude his thought out destiny without the other pieces of the Triforce. He seeked out Princess Zelda but to no avail, as she was hiding under a false appearance and name for seven years. He knew Link would come after him eventually, and he watched as he killed the evil inside the temples accross Hyrule. After Link had received all the Medallions from the Sages he sought after Ganondorf in his temple. Princess Zelda was kidnapped by him, and Link followed, in an attempt to save her and bring peace to the kindom of Hyrule. He succeeds in doing so, after killing Ganondorf with the power of light. He is sealed away into the Sacred Realm, whispering in his last words that he would destroy Link's descendants.

Ganon: Wind Waker
The Link in Wind Waker first encounters Ganon at the Forsaken Fortress, Ganon's hideaway and source of evil. In WW Ganon is slightly more muscular and some people believe he is more obese. This is obviously false as you can clearly see that what people consider "fat", is his bulging chest. He wears a neat delicate overcoat in this game, and his presence is much more noticable. Ganon has broken free from the Sacred Realm and is currently searching for Zelda's descendant and Link's. It is never said if the Link in this game is the Hero of Time's descendant, but what we do know is that Tetra is actually Zelda's descendant. Since the Hero of Time was long gone by this time, the Triforce of Courage had been shattered and scattered accross the world. An actual quote from the game goes as this,

"Link, do you know the legend of the Hero of Time? Once long ago, he defeated Ganon and brought peace to the Kingdom of Hyrule...A piece of the Triforce was given to the Hero of Time and he kept it safe, much as Zelda kept hers. That sacred piece is known as the Triforce of Courage. When the Hero of Time was called to embark on another journey and left the land of Hyrule, he was separated from the elements that made him a hero. It is said that at that time, the Triforce of Courage was split into eight shards and hidden throughout the land."

Link goes on a quest to find all these shards. The Triforce of Courage joins Link and the Triforce of Wisdom is already with Tetra, as she is the true descendant. In The Legend of Zelda: The Wind Waker, Link's sister Aryll is kidnapped by a giant bird called the Helmaroc, one of Ganon's main minions. This causes Link to have a hatred for the evil man. Ganon searches for the hidden Triforce's, and when he does find them he realises he is sent flying back into the Sacred Realm yet again, after Link finishes him. He fades out saying...

"The wind is blowing..."

Ganon: Twilight Princess
It has been confirmed that Ganon, along with Princess Zelda, will make an appearance in Twilight Princess, and that his connection with the Triforce of Power will have something to do with the events in the game. Wether he is the chief foe, or just on the sidelines, has yet to be revealed, however.