Bottle Locations:

Master Ore (Used to upgrade the Master Sword):

Miscellaneous:

Stamina

Scroll: Increases your stamina. Found in the Ice Ruins.

Net: Allows for catching bugs/fairies. Talk to the man inside the Bee marked house in Kakariko Village.

Bee

Badge: Turns all bees into allies. Give a Golden Bee to the man who gives you the Net.

Hylian

Shield: Blocks more attacks than the standard shield. Found in Turtle Rock.

Blue

Mail: Halves damage taken. Found in the Swamp Palace.

Red Mail: Further halves damage taken. Found in Lorule Castle

Hint Glasses: Wear these to find the Hint Ghost and give him play coins for helpful hints. Speak to the Fortune Teller in Hyrule.