Fairy Fountains - Scattered across Hyrule in one place or another are hidden fairy fountains. Use these to fill your energy or keep some for later. If you die and have a fairy in a bottle you will be completely revived without getting a Game Over.
In Gerudo Fortress there are a row of four crates in the front. Play The Song of Storms in front of these to uncover the Fairy Fountain. At the Desert Colossus there is a dried up oasis. On the elevated rock nearby play the Song of Storms in order to fill the oasis. A bunch of Fairies will appear. I guess this is a Fairy Fountain. Near the Goron's City on Death Mountain Trail is a place to bomb the wall. There is a Fairy Fountain inside.
In Zora's River there is an elevated cliff with a circle of stones, I can't remember now, but I think there was a rock there. Get rid of the rock to reveal a Fairy Fountain. You can access this as Young and Adult Link. To get to the ledge that leads to the cliff as a kid use the Cucco. As Adult Link, just walk up and climb onto the ledge that leads to the ladder.
In Zora's Domain there is an island in the water/ice right near the entrance. On the island play the Song of Storms to reveal a hidden chamber. Inside you will find a Fairy Fountain. There is a Fairy Fountain in an area with trees in the Northwest portion of Hyrule Field.
Big Faries - Now when I say Big Faries I don't mean the ones that give you the three spells and three enhancements but rather larger versions of the kind of faries you put in the bottle. These faries fill your magic and life completely.
In Hyrule Field, Zora's River Branches off you will find that it goes to a dead end. You will also notice that Navi will turn green on a spot in the water. Stand in that spot and play the Song of Storms. An animation like a big chest will occur and a Big Fairy will appear.
In Hyrule Field, just before Lake Hylia there is that square of fence. Bomb here to find the hidden chamber underneath. Inside you will find dirty pools of water. Navi will turn green near one. Play the Song of Storms to uncover the Big Fairy. Inside of the Gerudo Training Ground, just past the entrance, Navi will turn green on the floor. Play the Song of Storms in this spot to make a Big Fairy appear.
Inside of the Gerudo's Fortress there is a room where a pot is boiling over a fire. Stand in front of a mask on the wall and play the Song of the Sun. A big Fairy will appear.
If you enter the Royal Family Tomb in the Graveyard (the place where you got the Song of the Sun) Navi will turn green near a skull. Play the Song of the Sun and a Big Fairy will appear.
In the Lost woods you will encounter a pond with a warp to Zora's River under the water. At the edge of the pond play the Song of Storms to make a Big Fairy appear.
In the Shadow Temple there is a Ledge where you fight a Staffos in a room with guillatines in it. Play the Song of Storms and a Big Fairy will appear in the center of the platform.
The same island/pedistal where you get the Fire Arrow there is a spot where you play the Song of the Sun to make a Big Fairy Appear.
Deku Scrub Salesman - These are guys that sell you something, usually a green or red potion. Sometimes though they sell you Deku Nuts or Deku Sticks. I have a couple of these listed in the Walkthrough, but the following will become a listing of all of them.
Behind the Carpenter's Tent in Gerudo Valley as adult Link. Play the Song of Storms to open the secret chamber. Inside you will find two Deku Scrubs that sell you a green or red potion for 40 rupees. (These sure did come down in price since Link to the Past)
At the Desert Colossus, if you lift a rock near a circle of stones you will reveal a secret chamber with two more of these guys selling potions inside. In Death Mountain Crater, just near the broken bridge there is a rock, break it to reveal a chamber with Deku Scrubs. One will sell you Bombs for 40 rupees, another will sell you 30 arrows for 70 rupees, and the other one will sell you 5 Deku Nuts for 20 rupees.
As soon as you enter Zora's River you will encounter a circle of stones. Play the Song of Storms in order to reveal the secret chamber. You will find two Deku Scrubs. One will sell you a red potion for 40 rupees, and the other will sell you a green potion for 40 rupees.
At Lake Hylia there is a single gravestone between the two bridges. Open the Gravestone to reveal three Deku Scrubs. One sells you bombs, One sells you arrows, and the other sells you Deku nuts.
Use the Iron Boots to sink to the bottom just below Zora's Waterfall. (The one you play Zelda's Lulliby in front of) You will find several red rupees here. At the top of the drawbridge in front of the market there are a few red rupees. Inside Death Mountain Crater is a Platform all the way to the right from the entrance to the Fire Temple with many rupees on it.
There is a Gold Rupee in Goron City in the room with all the rocks in it at the very back and to the left.
There is a Gold Rupee in Kakariko Village in the clearing area past the tree in front of town. It is detectable with the Stone of Agony. Use bombs or the Megaton Hammer to find it. There is a secret chamber below the Circle of stone in front of the Goron's City. Inside you will find a chest with a Gold Rupee inside.
Shoot the Blue Spiders in Lake Hylia with the Light Arrow and get a Purple 50 ct. rupee.
In a grotto under a boulder on a ledge near Gerudo Valley you will find some rupees in the shape of an arrow that point to the northwest. Kind of odd. There's nothing on that wall. Infinite Rupees - get all the gold skulltulas and keep returning to the House of Skulltula in Kakariko to get another Gold Rupee.
Next to the bean selling man.
In the Lost Woods in the area near the "Forest Stage."
In front of Dodongo's Cavern.
Next to the Lakeside Laboratory.
In front of the Desert Collosus.
In the Graveyard near a wall to the left.
In the Kokiri Forest behind a house.
At the bottom of the ravine at the Gerudo Valley.
Inside Death Mountain Crater near the Triforce teleportation pedistal.
In the Lost Woods on the ledge across from the bridge you cross when you first enter/exit the Kokiri Forest.
