All the items that can be found throughout Hyrule are listed below along with their locations and uses. I didn't include the armor or weapons - I put them on seperate pages.
Bomb - The bomb bag can be found in Dodongo's Cavern for the first time. You can use bombs to blow up brown 'dirt' doors anywhere in the game.
Bombchu - This item works just like a bomb, but it can travel a distance before blowing up. They can be found in the market at night in a store in the back alley, in treasure chests, or you can win them in the bombchu bowling game.
Golden Skulltula Tokens - These golden tokens appear after you defeat a Golden Skulltula. If you collect 100 tokens, you'll be really rich. Visit the House of Skulltula after collecting every ten tokens for a prize.
Bottles - These bottles hold all kinds of things. Bugs, faries, milk, fish, blue fire and red, green or blue potions. There are four bottles hidden throughout Hyrule.
Fairy Ocarina - This ocarina will be given to you by your best friend Saria. You can play any song you learn on it.
Ocarina of Time - This ocarina will replace the Fairy Ocarina. It's just like the Fairy Ocarina, but this ocarina posseses some magic powers.
Heart Piece - These pieces of heart can be found throughout Hyrule. There are 36 pieces altogether, and some can be aquired when Link is an adult, or when Link is a kid.
Silver Scale - This Scale can be found in Zora's Domain as a child. It allows you to dive deeper underwater than you could before.
Golden Scale - This Scale can be found off a 12lbs fish. Catch one in the Fishing Pond. This item can be found ony as an adult.
Goron's Ring - This item will be given to you by Darunia, leader of the Gorons. Play Saria's song for him, and he will do a wacky dance and give you the ring.
Silver Gauntlets - These gauntlets can be found in the Spirit Temple. They allow you to pick up really heavy objects and can only be used by adult Link.
Golden Gauntlets - These gauntlets can be found in Ganon's Castle. They allow you to pick up objects over 5 times your size including boulders! Only adult Link can wear them however.
Claim's Check - You will receive this check from the BIG goron atop Death Mountain. After three days of receiving this, you will get the biggoron's sword!
Stone of Agony - You will receive this item from the kid in the House of Skulltula after finding 20 skulltula tokens. If used with a rumble pack, your controller will shake when a secret is nearby!
Gerudo's Card - You will receive this card from a Gerudo after finding all four carpenters in the Gerudo Fortress. It allows you to walk around Gerudo Valley freely.
Weird Egg - This egg will be given to you twice by the Cucco Girl. If you wait 24hrs, it will hatch into a cucco, or a pocket cucco.
Quiver - Adult Link will be able to carry 40 arrows with this item.
Lens of Truth - The Lens is found at the bottom of the well as a child. Search well for it, you need this item in order to continue in the game, and win the heart piece in the Treasure Chest Game as a child.
Magic Beans - A white bear-like creature sells these beans at Zora's River. You can only buy and plant these magic beans as a child. However, the prices for the beans go up each time you buy one!
Poe - These poes can be found in Hyrule Field, or in the graveyard, and they appear purple, with a frown on their face. Destroy one and capture it in a bottle. You can drink these poes to restore life, of depleat life.
Big Poe - These poes are found in Hyrule Field only, while on Epona. There are ten of them altogether. Unlike the normal Poes, these Special Poes are yellow and have a smile on their face.
Fairy - A fairy can be found almost anywhere. Capture them in a bottle, and they will restore your life fully if used. They will automatically restore you should you die, that's why they're so awesome!
Blue Fire - The blue fire will melt ice that appears reddish in color. You can use it to unfreeze King Zora when he freezes over.
Green Potion - A green potion will fully restore your magic, if you buy them in your bottle. In their own bottles, the potions will restore some, or all of your magic.
Red Potion - A red potion will restore all your life. You can find this potion at almost any potion shop. They're good for one drink, however.
Blue Potion - The blue potion fills your life and magic all the way. These special potions are found in the old hag's shop in Kakariko as an adult only.
Lon-Lon Milk - This nutritious milk can be bought from Talon as a kid, or, as I prefer, free from any cow. Playing Epona's song in front of a cow will reward you with free milk. The milk is good for two drinks, each restoring five hearts.