Fire and Ice Arrows
To obtain the Fire and Ice Arrows you must use the Ballad of Gales to warp into the Mother and Child Isles. It is impossible to enter this island without the Ballad of Gales. However, you must also wait until you have acquired the Master Sword as Great Fairy Mother will not give you the power of ice and fire until you have done so.
Upgraded Magic Meter
To get the upgraded Magic Meter you must sail to G4 or Two-Eye Reef. Nearby is a flock of sea gulls which of course means a Giant Octo is close. Sail there and you will be attacked. If you manage to defeat the Big Octo you will save a Great Fairy who will upgrade you Magic Meter.
The first wallet upgrade is located on your home island of Outset. To enter this fairy fountain you must have bombs, the Deku Leaf, and the Wind Waker. Climb to the top of the island and set the wind to blow to the west so you can float across the broken bridge. Inside the forest is a giant boulder that you can blow up to reveal the hole to the fairy fountain. Inside the Great Fairy will give a wallet upgrade which will allow you to carry up to 1000 Rupees.
Second Wallet Upgrade
This fairy fountain is located on Northern Fairy Island, or location A3. Enter the hole to find the fairy fountain. The Great Fairy inside will upgrade your wallet to hold up to 5000 Rupees.
Bigger Bomb Bag
To get the bomb bag upgrade you will need to sail to Eastern Fairy Island, C5. There will be a giant seashell building. If you blow up the boulder in its way then you can enter the fairy fountain. The Great Fairy will give you a bigger bomb bag, allowing you to hold up to 60 bombs.
Second Bomb Bag
Southern Fairy Island, F4, is the Giant Bomb Bag upgrade. Once again you will need to blow open the sealed entrance and then enter the fairy fountain. The Great Fairy inside will allow you to hold 99 bombs at one time.
To get a quiver upgrade you need to sail to Western Fairy Island, C1. There will be a switch on the island which can be smashed with the Skull Hammer. Doing so will lower the flame wall and allow you to enter the fairy fountain to get a quiver large enough to hold 60 arrows.
Large Quiver Upgrade
The large quiver upgrade is located on Thorned Fairy Island, D7. You will again need to use your Skull Hammer to smash the three switches on the island. This will lower the thorn barrier and allow you to enter the fairy fountain. The Great Fairy will upgrade your quiver so you can carry up to 99 arrows.