Hmm... This is a tough one. One one side, Ganon has the Triforce of Power, and is a very intelligent and formidible opponent. He has incredible strength and skill, not to mention his mastery of dark magic. On ther other side, Majora has powers that are not only mysterious but incredibly dangerous and destructive. He is unpredictabile and psychotic, and that combined with his incredible powers makes him a very deadly foe. All this being said, it's very difficult to determine who would win if they were to fight. It could go either way. I honestly can't decide.
Majora, that thing has so much power, I mean think about it. It could have forced a moon to destroy Termina if Link hadn't shown up. Let's put it this way, Majora is powerful no matter what form its in, Ganon still needs the help of the Triforce of Power to fight Link. And, Ganon tried to get the Triforce so he could become almighty and powerful, while Majora was already really strong. If the two were fighting in their "normal" states, Majora would win. Plus, to strengthen my point, Ganon only wanted to rule Hyrule, although he showed that he could do some pretty devastating stuff if he wanted to, Majora on the other hand wanted to destroy an entire region which shows that its merciless and psychotic.
I fell that Majora moves around so much and is so unpredictable that Ganondorf wouldn't be able to hit him, but I also feel that Ganondorf is powerful enough to block any of Majora's attacks.
Majora has strange powers that aren't ever explained while Ganondorf has extremely powerful dark magic along with the triforce of power to make him strong. I think that Majora would win because I don't think he showed the full extent of his power in MM and since we really don't know that much about his powers, he could be god-like compared to Ganondorf because we don't know how strong he is. In that case, I'd say Majora would win, although, if Majora really isn't that strong, then maybe Ganondorf could overpower him. In that case, Majora would probably destroy everything by bringing down the moon which I don't think Ganondorf can stop, in which case, Majora still wins (as Majora probably knows how to survive his own attack).
Ganon would win, majora could be killed with any sword. Ganon would turn majora to dust just like he did to the sage of water. Ganon is immortal and how can someone who posesses the triforce of power be turned into a deku scrub. He's the most powerful man in zelda.
I think Ganondorf would win, because the only thing that can actually defeat him is the Master Sword or Silver Arrows. Majora may be incredibly powerful, but he/she/it wouldn't be able to destroy someone who can only be killed by Silver Arrows or The Sword of Evil's Bane. I think there'd be a very, very long battle and in the end Ganondorf would defeat Majora and then he'd probably absorb his/her/its dark power becoming even more unstoppable.
It entirely depends on what you think Majora is and how you consider its power. Ganondorf's power is established and explained (well, except that it can differ a bit from game to game), but Majora's is a little more abstract.
I myself would say Majora, though. Yeah Ganondorf can only be slayed by the Master Sword, but that's not as relevant in something like this I think, because I almost look at the Master Sword as a plot device rather than a very important detail in the actual mythos. Ganondorf's immortality to anything except the Master Sword also likely derives from his possession of the Triforce of Power, which means it's essentially a direct blessing from the Goddesses.
My take on Majora is that it is a demon, or a devil. An entity of pure evil. And this makes him either a fallen god or an anti god. Because of that, I think it almost puts him on par with the Goddesses. He's probably not as powerful, but I think saying he's close is fair. And I think even if he's weaker than the Goddesses, putting him on above someone who only has some of their power also seems fair to me.
Another issue is how both are portrayed. Ganondorf in all the recent games is simply a man. Despite all his divine and/or sorcerous power, he's a man with ambitions trying to take over and rule. Even in the classic games, where Ganon is less human and is portrayed as the "King of Evil" or "Demon King", despite his amplified evil he's still only a ruler. But Majora is portrayed as the ultimate evil. The destroyer. The final evil. That kind of thing. His actual presence and role on the story is much more powerful, intimidating and malevolent. I think this shows an element of the creators' actual intentions, and that above all else is why I say Majora is the more powerful entity.
Difficult to answer because they both go through multipule forms. But there most powerful forms (presumbly) dueling each other would be EPIC.
If Majora is a deity (or a demon I guess now I think about it) like Axle suggests it would be hands down Majora as he/she/it would have next to limitless power. Ganon in monster form is called in some games "The King of Demons". But that's not really relevant in this because you wouldn't have a battle of the titles now would you?
If Majora isn't a demon, it would be a pretty epic battle but I would have to say Ganon, since the only thing that can kill Ganon is the master sword, or the silver arrows. Majora would win because his evil would over-power Ganon's evil.
This is all my opinion of course but as for my conclusion, it would be a long and epic battle but in the end the winner would be.............. Majora.
I would have to say Ganon. His power seems to far surpass Majora's, rendering Majora's magic virtually useless. Ganon has the Triforce of Power, giving him the upper hand on Majora. Also, Ganon's power has been demonstrated on multiple occasions. If he felt like it, he could probably do anything Majora could +more.