The Ganondorf fight has two main phases. During the first phase you need to deal 22 or more damage to Ganondorf then have Zelda hit him with a Light Arrow. Ganondorf will then knock Zelda out and the second phase will start. During the second phase you need to deal a certain amount of damage to Ganondorf without the assistance of Zelda. Once this damage has been dealt, Zelda will wake up and you can finish him off.
The most common strategy is to wait for Zelda to shoot a light arrow to stun Ganondorf. Then perform a jumpslash quickspin followed by 2 quickspins. After this, talk to Zelda right away and back off. Zelda will shoot a 2nd light arrow which will end the first phase in one cycle.
The fastest Ganon fight uses the Iron Boots although it is the hardest and most risky. Iron Boots are useful as they allow you to land a jump attack in a much shorter period of time, allowing you to get more damage in a shorter period of time.
Perform the Standard Strategy. After the 3 quickspins, position yourself so that you are in a straight line with Zelda and Ganondorf, and hold your shield. You can actually reflect Zelda's second light arrow shot right after she shoots Ganon, allowing you to get a little bit more damage in during the first phase. This guarantees that you can one cycle phase 2 using the Standard Strategy.
The easiest strategy (although not the fastest) is to wait for Ganondorf to attack you with his sword combo. This will allow you to parry him. After the parry, perform a jumpslash quickspin followed by a second quickspin. Ganondorf will then try to attack you again. Repeat these steps a second time to end the second phase.
If you did the Iron Boots Strategy during the first phase, you can redo it for the second. This will allow you to skip a cycle.
If you parry Ganondorf very late, you can sometimes squeeze in extra damage. This can allow you to finish the 2nd phase in a single cycle.
If you release target while shielding the light arrow from Zelda, it will skip a small cutscene of the light arrow reflecting off of the shield.