I think i've brought this one up a few times.. but i like it.. both involve the flooding of Hyrule (leading to windwaker)
1. A sad ending, Ganon takes over Hyrule completely .. as in, more and more towns go to him as you progress through the game (which is the complete opposite of what is expected to happen as you progress through a game), leading up to one ultimate conclusion in which Link is unable to defeat Ganon after all attempts, and Hyrule is flooded by the sages to block his evil.. hope is found, but is not fulfilled until windwaker
2. A happy ending, The game starts with Ganon in complete control of Hyrule, and the sages have began the process of flooding the world, Link and Zelda travel back in time in the Temple of Time back to when he had no control and stop his empire from rising.. meaning the flood would never need to happen.. this would probably cause a split timeline where the first leads to windwaker, and the other leads to a non-flooded futuristic zelda game that hasn't be created yet :P
EDIT: @totalwar: hahaha.. gotta love CDi
