There are many great fairy upgrade locations scattered across the game. Each great fairy will give you a unique and very useful ability to aid you on your quests. There is no order in which you need to visit the fairys. If you visit the wallet upgrade fairy in different orders you will get the upgrades in the order of lowest first. Here is a list and guide of all the great fairy upgrade locations in the Wind Waker.
1000 Rupee Wallet Upgrade – This one can be found right at the start of the game, on Outset Island. In order to access this you need bombs and your Deku leaf. Go to the location where you originally rescued the pirate girl. Use the Deku leaf to cross the broken bridge and then use the bomb to blow open the entrance to the fairy fountain.
5000 Rupee Wallet Upgrade – North fairy island (C-1) is where you can get the second upgrade. All you need to access this island are bombs. Blow up the stone covering the entrance, head inside and you have your final upgrade.
Bomb Bag Upgrades
60 Bomb Bag Upgrade – Eastern Fairy Island (E3) blow open the entrance with bombs and head inside to get a bomb bag that can hold 60 bombs.
99 Bomb Bag Upgrade – South Fairy Island (D6) as with the other fairy island, blow open the entrance with your bombs and head inside to get a bomb bag that can hold 99 bombs.
Arrow Quiver Upgrade
60 Arrow Quiver Upgrade – Thorned Fairy Island (G4) is the first location you will get an upgrade to your arrow quiver. You will need to have the Skull Hammer in order to smash down the pins to get access to the fairy fountain.
99 Arrow Quiver Upgrade – Western Fairy Island (A3) is the location of the final upgrade. Use the Skull Hammer to smash down the pins and head inside to get the final quiver upgrade.
You now have all of the upgrades from all of the great fairy upgrade locations. The game should be a lot easier for you now that you will likely never run out of supplies.