The Yuganon notes I wrote for a post on Zelda Universe. Most of it covers A.I. behavior.
When the fight starts, move left or right a touch to lure him into a lunge attack for some easy hits. There are two different strategies to combat the basic attacks that Yuganon throws in phase one.
You can be extremely aggressive and get up in Ganon's grill. The standard lunge can be dodged by being super close and preferably rotating clockwise so that you stay near his non-trident hand. To avoid the slash attack, you basically slash to recoil off of his trident, just barely out of reach as long as you aren't backed up against a wall. You still want to be attacking his non-trident side.
You can lay back a bit. You'll be more vulnerable to the standard lunge, but should be able to easily avoid the slash attack with patience.
Either way, watch out for Ganon's double slash attack. It's easy to dodge when you know it's there.
With maybe 1/4th of his health gone, Ganon will start using a teleport, or a teleport into a slash attack. You can read where he teleports by watching the particle effect that pops up when he teleports away: he will spawn in the same general direction as the particles move to. He will also use a charged lunge attack that can be avoided easily by standing closer to the opposite wall and moving roughly parallel to the trident.
At 1/2 of his health gone (critical health), Ganon will start to flash red, and will introduce two more attacks, as well as teleport around more frequently. The first attack is one where various balls will shoot lightning down causing an explosion on the ground. This attack is easily avoided by simply making sure that you are moving. Yuganon will typically use this attack as soon as he reaches critical health, but sometimes it will be delayed if he hits critical health while in the teleport->slash pattern.
The second is Ganon's famous trident toss, which shares the same sort of charge animation as the charged trident lunge. The trident toss will replace the charged trident lunge, but occasionally Ganon will throw in a charged trident lunge immediately following a trident toss. Avoiding the trident toss is a little tricky: If Ganon is standing next to a wall before the trident is thrown, you can stand at the opposite wall and safely avoid the attack. Otherwise, staying close to Ganon will allow you to predict how the trident will move since about a few seconds after Ganon throws the trident, he teleports, and you can use the particle effect to guess where he will spawn (and consequently the point that the trident will home in on when he catches it). There is a safe spot to stand near the trident-less hand such that you won't be hit when he tosses the trident, allowing you to view the particle effect.
After phase one is the second and final phase, and arguably his easier phase. There are three parts to this phase:
Part 1: Ganon will always start with a dead man's volley. If you swing and miss the ball, you won't be able to deflect it back, so you will need to focus and be patient with your swings. If you miss, you can try to merge with a nearby wall, but don't rely on this. After Ganon is hit and you collect the light arrows, simply shoot his front then behind, and hack away when he pops out of the wall. With the Lv1 Master Sword, this will take 8 swings (which suggests that the Lv1 Master Sword deals extra damage for this fight). When Ganon pops back into the wall, you will want to merge into the corner of the wall to avoid the fire bats. Unmerge once or twice to conserve magic.
Part 2: Same sort of deal as part 1, but the volley ball will move faster this time. Shoot once with the light arrow to force Ganon to charge at you, unmerge, merge behind him.
Part 3: After you dodge all the bats from the last phase, you are home free. This time, you are allowed to spam your sword slash to return the two volley balls. Fire the light arrow, stab once more, done.
