Ganondorf, the demon king of the Gerudo was probably not always evil, infact his intension were probably just missled. But to understand that you have to understand the major idea that Ganon and Ganondorf are two different entities. And this is an idea that takes a bit of an open mind so bare with me. First of all, Ganon and his control over the Triforce of Power (ToP) curropted it with a demonic energy that stuck with it. Even after Ganon 'died' his energy still existed in the ToP. This Curroption skewed Din's energy. Din being the creator of not only land, but the Gerudo as well, cause the Gerudo's civilization to loose it's solidity. In other words, the Gerudo were a casualty of Ganon's curroption. The Twinrova are many generations old ( 400 years according to OoT) and watch the decline of there land into desert, Thus when conditions were unlivable, they moved to the the Gerudo Fortress at the edge of the desert were it was possible to live, Hyrule river and lake being decent sources of water. All the while gaining the reputation as thieves as they had to steal to survive. With Ganondorf's birth, they ( Koume and Katake) had the idea that with the ToP they would have the power they needed to restore the Gerudo land to its past glory. But without the power as a nation to take it, they planned to use political power, taking young Ganondorf under there wing ( or broom ) and teaching him to hate Hyrule for having such wonderful living conditions while being so forsaken themselves. With Ganondorf taking up the title of King of the Gerudo, the Twins took there place as Ganondorf's advisors, and began allowing Ganondorf to get close to the King of Hyrule, slowly gaining political strength in the form of the Kings favor. Ganondorf did as the Twinrova instructed with the goal of obtaining the ToP. ( Enter Young Link With the three Crystals. ) Link unlocking the master sword left the ToP for Ganondorf to steal, which he did successfully in Link absents, HOWEVER, Ganon's lingering power was overwelhming, possessing Ganondorf as Ganon's evil wishes and Ganondorf's selfish goals became one. With Ganon now living within Ganondorf and sponcering his actions, Ganondorf forsaken Twinrova and the Gerudo people and went to finish what the original Ganon had started, sealing the sages away and taking the land of hyrules as his own.
Ganondorf himself is however not aware that Ganon exist inside of him. All events that the title 'Ganon' has been used within a boss battle with Ganondorf was after Ganondorf was in an unconcious state, when Ganon could mentally take over. Proof of this is shown in OoT, TP, and even in Super Smash brothers Brawl, after his Final Smash is used, he appears dazed for a momment before he comes to.
I'm sure I've left alot out, but gimme some feed back, what do ya think?

Ganon/Ganondorf has always been twisted and evil. I bet he hid his parent's TV remote and locked his nana in the basement. But we will never know until he makes it either to Oprah or Dr. Phil. Then he'll spill some yarn about how his father never loved him because he never went to Gannon's track meets. He'll cry on Oprah's shoulder, right before sending her to another dimension and everyone has a good laugh about how she totally bought his sob story.

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Ganon could still know about it. I don't think he would really care - his soul was consumed by a lust for power before ever entering the temple. He got the triforce of power because that is all he knew being the Gerudo king.

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All Kokiri who leave the woods become Skullkids - lost souls of the Forest... There once was a kokiri. He was friends with Link and Saria. When she became the Forest sage he ran. After saving Hyrule the Hero of Time set out on a search. He found an old friend and helped him become happy. That is what happened to Mido. He may have later guided Link in TP.

I agree on the part where Ganon and Ganondorf are two different entities. I even think they are two different persons. Ganon might just be a word for evil. So when Ganondorf dies he just turns into pure evil namely Ganon.

You could, by that theory, suggest that Ganon has always existed, as a force of evil necessary to balance the force of good in the world. The ol' Castlevania theory.

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You're bringing some new insights and depth into my favourite character/bad guy of all time.

Though I could see where you're coming from, I'd like you to take this into account too:
In OoT, Ganondorf did not change into Ganon when he was unconscious. When he looked like he was unconcious, he tried to collapse the tower onto Link and Zelda. When they make it 'safely' outside, the tower collapses on itself, burying Ganondorf under piles of rubble. However, when he manages to trow the rubble off of himself, he is clearly not unconcious. Merely overflown by rage and maddened by spite. Then he uses the power of the Triforce to transform in himself in the great beast Ganon, cleverly named by discarding the German village off his normal given name, probably some second name he used with his friends when he was still attending Hogwar... other story, sorry.
He was well and fully aware that he turned himself in that minotaur-like being.

In TP, he again fueled himself with rage and the Triforce of Power, turning in the Evil Beast. And again he wasn't unconcious.

Ganondorf is just your normal, next door power-maddened Dark and Evil Overlord that happens to come across the God's power.

I'm wondering, where did you get the whole Gerudo story from? Cos I have never read anything about how the Gerudo desert was slowly formed etc and Twinrova's motives. Did I read over that in OoT or..?

What I came up with was more like a backround leading up to a fanfic of mine ( which I am 2 chapters in ). The backround story of the Gerudo themselves, was pretty much fabricate by me. It fits together well and flows with OoC and TP... In other words, it is by no means fact.

As for him not being unconcious, in OoC, When he emerges from the rubble, his eyes lack a pupil. When people are unconcious, theres eyes tend to roll back into their head, the blank eyes are commonly used throughout animation to show a loss of self, or unconcious state.
In TP, he becomes the Ganon beast after Minda pwns him out of Zelda. There isn't any proof whether Ganondorf meant to become the beast form or if it happend independently of himself, so for the sake of the arguement, it can be manipulated in either way.

The lovely thing about Zelda is that is rather open ended and mulitple facts can be manipulated to fit the arguement. I've just tried to fit it together in a way that makes sense to me, and makes sense for the up comming fanfic.

Thanks for the comments

You are indeed right, it can be interpreted in several ways. Me, I like to think the lack of pupils is because of the rage, magic and desperation he feels, throwing himself in one last Body Of War-like spell.
I wish you good luck on your fanfic. :)