I think it comes down to MM or TWW. In the latter Ganondorf was such a deep and pensive character. Years of being sealed away by the sages in the Sacred Realm made him more cautious and thoughtful in his words and actions. No longer does he truly want to destroy Hyrule but rather reform it. He maintains that the Gods betrayed the people of the land and that he is there to reform law and order and establish prosperity.
As deep as Ganondorf in The Wind Waker may be, Majora's Mask is an allegory unto itself with its dark theme, historical allusions, and deep seated symbolism. Majora's Mask is a very depressing game. The world of Termina is doomed within 72 hours and the masses are ignorant of the terrible fate they will soon meet. At the head of this dim future which Link must halt are the moon as well as Skull Kid. I find it extremely intriguing that Nintendo chose to have the moon be the object set to demolish the world in Majora's Mask. In many ancient religions, the moon was an important symbol-for some representing the harvest while for others a sign of the apocalypse. What the moon's portrayal in MM most reminds me of, however, is the poem Romance de la luna luna by Federico Garcia Lorca. In this piece, the poet refers to the moon as something that will take your life away if you stare at it too long. The Skull Kid was another highly symbolic element of the game which contributed to its profoundness. He wasn't inherently evil as his portrayal in Ocarina of Time highlights, however, the power of the mask perverted him. I interpret this as a metaphor of the corrupting influence society has on children.
Great thread. I look forward to reading other peoples' responses in the near future.