Here is a guide to defeating every boss in the Legend of Zelda: Wind Waker.
Dragon Roost Island Boss
This boss is rather easy to beat. At first all you will need is the Grappling Hook. Aim it at Valoo's dangling tail on the ceiling and then rock back and forth while attached to it. Afterwards, swing off and repeat it 2 more times until it's shell cracks open. Then put away your grappling hook and take out your sword. The boss will then lunge at you. Dodge these attacks and attack its eye when its stuck near the ground. Attack it around 3 or 4 more times to finish the job.
Forest Haven Boss
This boss is a giant carnivorious plant. To beat it, you must first get it off of the ceiling. Run around the arena and try to take down the vines with your boomerang. One of this boss's strengths is its ability to make a wall of vines burst out in front of you. Try to dodge these or you'll lose a quarter of a heart. It can also drop vines that were hovering above you, watch out for those too!(1/4 of a heart damage). After knocking all of the vines out, it will fall to the floor and its center will be exposed. Run up and unleash a series of sword combos to beat it. It wont take many hits to beat it, but be quick. If you take to long you'll be eaten by the plant, losing one full heart. Make sure to backflip out of the flower quickly if it starts to close.
Tower of Gods Boss
This boss is a whole lot like Bongo Bongo from Ocarina of Time. You'll need your newly aquired arrows and bows to defeat his boss. And don't worry about running out of arrows - the boss will drop some every now and then. To beat this boss, target and shoot and the red spots on the floating hands. After shooting each twice, they will turn over and the head will open it's mouth. Throw a bomb quickly in, or else you'll have to do it over again. Throw 3 bombs in the mouth to win the battle and claim your prize.
Forsaken Fortress Bosses
1) Phantom Ganon: Phantom Ganon is the first boss of the Forsaken Fortress. He is relatively easy to beat though. He is quite like the Phantom Ganon in OoT also. However, he can materialze in different places around the arena. He will first shoot energy balls. You need to hit these with your sword with good timing. It turns into sort of a tennis match. When you hit him he'll lower near the ground. You'll need to attack him quickly once he's down near the ground. Though he can attack you with a whopping 2 heart sword attack. Whenever he disapears look around the arena for him again. Once you beat him, you'll win the Skull Hammer, which is quite important in battle two.
2)Helmaroc King: This bird is pretty tough. It'll try to hammer you into the ground with its beak(1/2 a heart damage). Dodge these and he'll get stuck in the ground. Smash his head in with the skull hammer. The battle will get tougher the more times hes hit. Give him 3 good hammer thackings to break his mask and he'll get pretty rough. He'll begin to try and rake you with his talons and blow you into the spiked walls with powerful wind gusts(Run against these winds to avoid damage). Wait awhile until it tries the beak attack again, jump out of the way and give him a good whack-a-mole hammer strike again. His mask will then break. This will cause him to become quite vunrulable. Wait for another beak attack. Then slice'n dice his head with your sword after he's stuck. Keep attack its head until it dies.
Earth Temple Boss
This boss is a giant Poe. You need to use your Power Bracelates and Mirror Shield to make this boss vunrulable. Find a patch of light shining on the ground and go over there. Shine your mirror shield towards the Giant Poe until it becomes solid. Then run forth and pick it up. Now throw it into a spiked pillar on the wall, making it a bunch of tiny poes. Destroy all of these by any attack you have, primarily the sword, before they regroup again. As you attack more of these, the huge Poe's attacks will become more intense, it will breathe fire from its lantern and even try to squash you, causing Link to lose his sense of direction for a bit.
Wind Temple Boss
This boss is quite like a snake. Except for the whole evilness and sand diving part. You must watch out for the hole that appears in the center of the quicksand, or you'll be eaten briefly. Also, little baby molgeras will be jumping around in the sand. Killing these will get you some quick hearts and save you a lot of grief(they have a nasty habit of getting in the way of you targeting the tongue). To win, you must wait until it exposes it's open mouth. Then, hookshot Molgera's tongue and get it out of his mouth. Then slash it as much as you can before it goes back into the mouth. After a little tongue slicing. It will jump out of the sand and then jump back in, most likely hitting you. Repeat the process a few times to win.
Ganon's Tower Bosses
The first section of the Ganon Tower bosses are four that you've beaten before in the game. Then its on to the big guys.
The first boss is a 3 stage Ganon Puppet: The Marionette, Spider, and the Snake. Together, they are the toughest boss yet, so get ready for a multi-item battle! Marionette-Phase 1-The Marionette is easy enough. It has a powerful one heart punch attack, but otyher than that, the only trouble is the bats, who give you magic when you kill them. To beat this guy, take out your boomerang and target as many strings above puppet Ganon as you can. Most will just slow him down, so your chief concern is to knock down the one holding his tail up. Once this is broken, shoot the blue ball dragging on the ground at the end of the tail with the light arrows. Then you'll have to wait while Ganon goes and reattaches the strings. Hit the crystal Ball on the tail 3 times to win.
Spider-Phase 2-This boss is pretty easy too. To beat this you'll either need luck or agility, preferably both. First, kill the three bats that it dispatches whenever it goes up. Then quickly look up to see where the crystal ball is and run to there. Then shoot the crystal ball. Do this three times to win. However, if you don't have time to look up, try to go to a spot that the legs wont fall, and see if the tail is close to there when he comes down. Shoot the the crystal ball 3 times to win.
Snake-Phase 3-The snake is by far the aggresor of the 3 Puppet Ganons. There'll be those annoying spiked balls that jump on you and slow you down. One sword whirl will take care of them when there on you. The Snake will thrash around everyway to hit you can cost you damage. However, this is his weakness. He often swings around in circles over and over. All you have to do is time the moment when his crystal ball on the tail is in perfect alignment with you and shoot your light arrows. All it takes is good judgement. Do this 3 times to win. Now it is time for the ultimate challenge, Ganadorf himself.
Ganadorf
Ganadorf is the most aggresive boss you'll meet in the game(which is the reason he's the final boss) Every hit you take from him is a full heart, so watch out! First you must rely on tactics and patience to score any damage on him. you can either wait to do your parry attack when the jagged A button appears, or wait for Zelda to hit him with the light arrows. The parry attack is an excellant distraction for Zelda to get a light arrow in. After 3 light arrow hits to him, he'll swat down Zelda, knocking her out. Now you must fully rely on the Parry Attack. This will leave him stunned and open to beating with the Master Sword. After 7 master Sword hits, Zelda will be back and ready for action. Now you have to distract Ganadorf, so that Zelda has a chance to nail him with a light arrow. To do this, use you shield and reflect the blow to Ganadorf. The easiest way to do this is to target Ganadorf and put up your shield. Angle yourself so you partially facing Zelda and partially facing Ganon(they should both be in front of you in the camera). Don't move a lot so Zelda can target you and not miss. Then she'll fire a light arrow at you, with which you will reflect into Ganadorf, giving him some damage. Keep your shield up though, or you'll get hit instead! After he's hit with a light arrow, quickly run up(or he'll recover) and slash him for the final blow. Then sit back and watch the ending.