Upgrades
Here are the upgrades for all of the applicable items.
Deku Seeds:
#1. In the Lost Woods, entering from Kokiri Forest, go to the right one room when you enter. Then you will see a golden target hanging from a tree. Shoot it in the middle with your Slingshot and score three scores of 100 and it's yours.
#2. Go to the Market as Young Link and enter the Archary Game. Your prize will be a Deku Seed bag if you hit all 10 rupees.
Quiver:
#1. In Kakariko Village, go to the archery game and hit all 10 rupees and get a new quiver.
#2. Go to the Archery Range at Gerudo Fortress and score 1500 or more. The lady will then give you a new quiver.
Bomb Bag:
#1. Go to the Market and go to the Bombchu Bowling game. One of the random prizes will be a new bomb bag.
#2. In Goron City, stop the big rolling goron near the sign on the same level to get a new bomb bag.
Deku Seeds:
#1. Go into the Lost Woods. Go in these directions entering from Kokiri Village: R, L, R, L, L. Now go over by the butterflies. There will be a hidden grotto in the bushes. Down there are a bunch of Deku Scrubs. If you have a mask with you, they will give you their opinion of the mask. Get the Skull Mask and put it on for the Deku Scrubs. They will like it. Talk to the big Deku Scrub for the upgrade.
#2. Go back to the secret grotto in the bushes. Put on the Mask of Truth after trading all four masks. They will like it. Talk to the big Deku Scrub for the upgrade.
Deku Sticks:
#1. Go into the Lost Woods from Kokiri Forest and go L, L. Go to the end of the room and there will be a Deku Scrub there. He will sell you the upgrade for 40 rupees.
#2. ???