Upgrades will allow you to carry more of your expendable items or give you newfound powers.

When you've collected 10 Gold Skulltula tokens, go to the House of Skulltula in Kakariko Village and talk to the kid that's been freed from the curse. He'll give you the Adult's Wallet. This will allow you to carry up to 200 rupees.

When you've collected 30 Gold Skulltula tokens, go to the House of Skulltula in Kakariko Village and talk to the kid that's been freed from the curse. He'll give you the Giant's Wallet. This will allow you to carry up to 500 rupees.
   
In Adult Link's world, the house the carpenters were building in Kakariko Village will be completed, and the shooting gallery guy from the Hyrule Market has moved in there. This time you can play the game with your Fairy Bow. Shoot every target to win the Big Quiver, which allows you to carry up to 40 arrows.
   
If you can win 1500 points on the Gerudo's Fortress Archery Range, you'll get the Biggest Quiver, which will allow you to carry a maximum of 50 arrows. Good luck with this, because (in my opinion), this is the hardest damn item to get in the entire game. Getting all of the pots on the first pass, and then hitting those three targets in the middle for as many 100 point scores as possible on the return pass.
NOTE: You can reverse the order in which you obtain the quivers. If you beat the Gerudo Archery Range first, you'll get the Big Quiver from there, and then you can get the Biggest Quiver from the Kakariko Village Shooting Gallery.
   
You'll find the Bomb Bag in a room in Dodongo's Cavern. It's inside a large treasure chest and isn't too hard to find if you just explore enough of the dungeon. The Bomb Bag will allow you to carry 20 bombs.
   
On the mid level of Goron City, you'll find a sign saying that "Hod Rodder Goron" might give you something great if you can stop his "wild rolling". Hod Rodder Goron is rolling around this level. Use a bomb to stop him near the sign. You'll get the Big Bomb Bag, which will allow you to carry up to 30 bombs.

The Biggest Bomb Bag is one of the items you can win from the Bombchu Bowling minigame in Hyrule Market. It will allow you to carry up to 40 bombs.
NOTE: If you beat the Bombchu Bowling game and win the Bomb Bag before you bomb Hot Rodder Goron near his sign, you will get the Big Bomb Bag from Bombchu Bowling and the Biggest Bomb Bag from Hot Rodder Goron.
   
After you get the Golden Gauntlets, leave Ganon's Castle and pick up the big vertical column with the moon on it that's just outside his castle. (It's close to where the Fairy Fountain was in child Link's world.) You'll reveal a cave to a Great Fairy Fountain that will increase your Defensive Power. All damage from enemy attacks will now be reduced by 1/2.
   
Deep in the Lost Woods are a couple of boulders that can be destroyed with bombs. One of them leads to a room with two Deku Scrubs. Beat them and one will offer to upgrade your Deku Nuts for a cost of 40 rupees. Accept and you'll be able to carry up to 30 of them.
   
Way off deep in the Lost Woods is an area with two Deku Scrubs, a dead tree, and some high grass with several butterflies floating around. If you walk in the tall grass near the butterflies, you should eventually fall into a hidden hole. This puts you in a cave with a sign that identifies it as "The Forest Stage". Put on the Mask of Truth and walk out onto the stage. A bunch of Deku Scrubs will pop out of the ground and judge your "face". The leader of the Deku Scrubs will then show up and offer to upgrade your Deku Nuts so that you can carry up to 40 of them.
NOTE: You can reverse the order in which you do these two tasks. If you take the Mask of Truth to the Forest Stage first, you'll get the 30 Deku Nuts upgrade, and you'll get the 40 nuts from the Deku Scrub beneath the rock.
   
Head left after entering the Lost Woods and go past the Skull Kid's area. You'll see a target hanging from a tree in the next area. Shoot the center three times in a row with your Slingshot, and a Deku Scrub will pop out and give you a Deku Seeds Bullet Bag. It will allow you to carry up to 40 Deku Seeds.
   
Go to the Shooting Gallery minigame located in Hyrule Market (only open during the day) and try your best to win. Get a perfect score, and you'll win another Deku Seeds Bullet Bag. Now you can carry up to 50 of them.
NOTE: You can reverse the order in which you do these two games. If you beat the Shooting Gallery first, you'll get the 40 seeds bag from there, and the 50 seeds upgrade from the Deku Scrub in the Lost Woods.
   
Take the left path after you enter the Lost Woods and go one area past the Skull Kid's room. You'll be in the area that takes you underneath the bridge that leads out of Kokiri Forest. Go to the end of this area and beat the Deku Scrub. He will offer to upgrade your ability to carry Deku Sticks for 40 rupees. This will allow you to carry up to 20 of them.
Just like with the Mask of Truth and the Deku Nuts (see above), take the Skull Mask to the Forest Stage in the Lost Woods. Walk onto the stage with the Skull Mask on and the Deku Scrub leader will upgrade your ability to carry Deku Sticks, so that you can hold up to 30 of them.
NOTE: You can reverse the order in which you do these two tasks. If you take the Skull Mask to the Forest Stage first, you will get the 20 Deku Sticks upgrade, and the 30-sticks upgrade from the other Deku Scrub.
   
After you've rescued all four of the carpenters being held prisoner in the Thieves Hideout, you'll be given the Gerudo's Membership Card by the Gerudo's leader. This will allow you to freely explore the Gerudo's Fortress without getting attacked or thrown into jail.
   
On the lowest level of Goron City, stand on the floor mat in front of the closed door and play Zelda's Lullaby on your ocarina. The door will open. Enter and stand in front of Darunia, the Goron's leader. Play Saria's Song on your ocarina and he will give you the Goron's Bracelet when he's done dancing. This will allow you to pick up Bomb Flowers, which were too heavy before.
   
In young Link's portion of the Spirit Temple, after you find and beat the miniboss with the axe, exit the room and you'll be outside on one of the Desert Colossus's hands with a large treasure chest. Open the chest to get the Silver Gauntlets which will allow adult Link to move heavier objects than he could before.
   
You can find the Golden Gauntlets in the "Shadow Temple" portion of Ganon's Castle. Use the Lens of Truth to find hidden pathways and light up torches with the Fire Arrows. The Golden Gauntlets will allow you to pick up the really large vertical blocks with the moons on them.
   
Near the Fire Temple entrance in the Death Mountain Crater is a doorway that is blocked off by boulders that can only be destroyed with the Megaton Hammer. Once you have the hammer from the Fire Temple, break the rocks and enter the door. You'll be inside a Great Fairy's Fountain. This particular Great Fairy will double your Magic Meter.
   
In Zora's Domain, go to the top of the waterfall (accessible from King Zora's chamber) and ask to play the Zora's minigame. He'll throw some rupees down into the water below. Retrieve all of them in the time limit to win the game and receive the Silver Scale as your reward. This will allow you to dive deeper underwater than before.
   
As Adult Link, go to the Fishing Pond at Lake Hylia and capture a 15 pound fish. Keep it and ask to have it weighed. You'll get the Golden Scale as a reward, which lets you dive even deeper than the Silver Scale.

The Sinking Lure is a special item you can find at the Lake Hylia Fishing Pond as Adult Link. I have most often found it just by running through the reeds along the edge of the area's wall, but sources claim it can also sometimes be found other places, such as near the big rock, the big log, or in the lilypads. This lure sinks to the bottom of the pond and makes catching fish easier, but it's considered cheating and you won't get any prizes for any fish you catch with it (unless you use a glitch to make it legal - go to the fisherman and choose "Let's talk about something else".)
   
Climb all the way up the Death Mountain Trail to the peak. To the left of the sign (where the Owl is sitting) is a very obviously breakable wall. Bomb it open and talk to the Great Fairy in the fountain inside. She'll give you the Spin Attack, which is a sword technique that uses up part of your magic meter (which you'll receive automatically with this skill, too).

When you've collected 20 Gold Skulltula tokens, go to the House of Skulltula in Kakariko Village and talk to the kid that's been freed from the curse. He'll give you the Stone of Agony, which is only useful if you have a working Rumble Pak installed on your controller. It will cause the controller to rumble whenever you get close to a secret area.
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