There is a bunch of cool stuff you can get at the Three special Farie Fountains. They are listed here:
1. Get the Flippers from Zora, then go to Lake Hylia. Swim to the island in the center, and go into the cave there. you will see a pool of water. Walk up to it and press B repediatly. It will ask if you want to throw rupees in. Say yes, and throw in a certain amount(it works faster if you throw in 100 rupees each time). Keep doing this and you will see a big farie appear. She will make it so you can carry more arrows or bombs. Once you get to 60 or so, you can't do this trick anymore, but it's good for you arrow-happy people out there.
2. *Note* You need Zora's Flippers to do this.
Head up to Zora's Falls, but don't go in it. Instead, swim over to a water to the left. You can walk through the center of it. You will come to a pool of water. Walk up to it and press B. It will ask if you want to throw something into the pool. Say yes, and you can select an item in your inventory to throw into the pool. After you throw an item in, a Big Farie will appear, and ask you if it's yours. Say yes, and you get it back. This doesn't seem really special, but try throwing your sheild into the pool. When the farie ask if it's yours, say yes, and your small sheild will be upgraded to the Red sheild, which can be bought at a shop in the dark world much later in the game, in the middle of nowhere, and it cost 500 rupees. So best to get it now. The Red Sheild is good since it repels small fire balls. Next, throw your boomerang into to the pool. After saying its yours, you will get it back... only that its upgraded to the Magic Boomerang, which flys faster and has longer ran!
ge. Still havn't had enough? Throw an empty bottle in, and the farie will fill it up with Magic Potion for free. Neato!
3. In the Dark World, after you get crystals 5 and 6, go to the bomb shop, which is Link's House in the Light World. The guy there will have a Super Bomb for sale. Buy it, and head toward Ganon's Pyramid. But be careful! Jumping off any cliffs or pressing B will activate the Super Bomb, and you have to go buy another one. Once you reach the Ganon's Pyramid, start walking up it. You will see a big crack in the wall, go over to it, and activate the bomb by pressing B. The explosion will blow open the crack. Go inside. Once again, you will come to a pool of water. Just like the other on, you will be able to toss stuff in, sometimes getting an upgrade. This time, throw in the bow, and you will get silver arrows, neccesary to defeat Ganon(Who is about as about as fat as the farie you talk to). Next, throw your sword in, when you get it back, it will be upgraded to the Gold Sword, the highest level.
Final Boss Tactics
When you get to the last boss, here's how to defeat him. Hit him a couple of times with your sword. He should throw his dagger at you. Try to avoid it. Do this another time. The third time you do this, he will twirl his dagger. Little fireballs will form around it. The balls will expand. Soon they will turn to fire bats. These bats take away 2 hearts. Try to avoid them. Keep hitting him with your sword. Do this step 3 times. When you finish, his dagger will be gone. Now his usual attack will be a power stomp that lets out a fire bat, that will make fire balls in its path. When he stomps, the floor will cave in on one side. If you drop through this, there will be 2 chests with treasures to help you. He'll stomp 4 times. Then the lights will go out. The 2 torches at the end of the room will go out. Light them with your torch or fire rod to see him. Hit him with your sword, then he will freeze. Quickly equip your bow and silver arrows. Shoot him once. The lights will go out again. Light them a second time to see him again, and hit him with your sword again. Equip your bow and shoot him with a silver arrow. Do this 1 or 2 more times and he will be defeated. A door will open and a bridge will appear. Go in the door to receive the tri-force. You have conquered the game!
Get 20 rupees from picture
When you are in the village,go to the house with the lady that has an orange dress.When you get inside pull on the Mario Picture and 4 blue rupees should pop out.
Get the 4th Magic Jar
Beside the desert in the light world, there is a man who sits by a sign and he says to leave him alone. When you are nearing the end of the game in the dark world, in the village in one of the demolished houses, there will be a chest. You can't open it, so bring it to that guy in the light world who wants to be left alone. He turns out to be a theif and he will pick the lock for you, and inside the chest is the last magic jar.
Get the Magic Powder
In the light world, when you are in the dark forest, you will see a rotted mushroom, you are allowed to put it in your item stash. It doesn't do anything, but take it and go to the witch who is brewing something beside the potion shop. Give the mushroom to her and she will say that she will give you something in return. So go in the shop, and beside the little guy sitting there, is a bag of magic powder.
Get the quake medallion
In the dark world go to the man selling stuff which in the light world it would be the witches hut.But don't go in instead go over to the right and go up and lift the object and follow the path. After a ways you will see a sign that is warning you not to throw anything in the circle of stones. Go to the left and you will see the circle of stones pick up the skull beside the circle and throw it in and a beast will come up and say if you leave him alone he will give you a presant. After he throws out the medallion go grab it. If you throw the skull in there again he will just spit a fireball at you.
Infinite Rupees
Go to lake hylia near where the icerod was found lift the large grey stone to find a passage inside are 20 rupees under pots go outside and come back in. The rupees are there again.
Items from the Fat Ferry
Near the end of the game in the dark world, you will see in the pyramid that there is a crack in it for a bomb to blow up. An ordinary bomb wo'nt do the trick, but a super bomb will.
Go to the guy near the village selling bombs. He will have a big green one to sell to you, go and buy it, but be carefull, since it is so big, you cant carry it, you have to drag it to the pyramid.
When you get to the pyramid, releace the bomb in front of the crack. It will blow a hole in the wall. Enter to meeet the fat fairy who will tell you to throw items into the pond. The only items you can throw in are your master sword, your arrows, and an empty magic jar. She will give you a #4 sword, silver arrows, and fill your empty jars with magic potion.
The Flute and the Duck
Once you have the flute, if you play it in front of the weather vane in Kakariko, the duck will come and help you. He can transport you to many locations. Here they are:
#1 Death Mountain
#2 Witch's Hut
#3 Kakariko Village
#4 Link's Cottage
#5 Warp Tile South of Eastern Palace
#6 Warp Tile in Desert
#7 Swamp Ruins
#8 South of Lake Hylia