Best deals are bolded
= As a kid =
Name of the Store: Kokiri Shop
Location: Kokiri Forest
Hours: 24 hours a day
Sells:
Arrows: 10 arrows for 20 rupees, or 30 arrows for 60 rupees. You need a Quiver.
Deku Nuts: 5 nuts for 15 rupees, or 10 nuts for 30 rupees
Deku Seeds: 30 seeds for 30 rupees. You need a Deku Seeds Bullet Bag.
Deku Shield: 40 rupees. This is the only store that sells the Deku Shield.
Deku Stick: 1 for 10 rupees.
Recovery Heart: 1 for 10 rupees.


Name of the Store: Bazaar
Location: Hyrule Market
Hours: morning/afternoon/evening
Sells:
Arrows: 10 arrows for 20 rupees, 30 arrows for 60 rupees or 50 arrows for 90 rupees. You need a Quiver.
Bombs: 5 for 35 rupees. You need a Bomb Bag.
Deku Nuts: 5 for 15 rupees.
Deku Stick: 1 for 10 rupees.
Hylian Shield: 80 Rupees initially, but if you show Zelda's Letter to the guard at Death Mountain entrance in Kakariko, you will get a discount. The price goes down to 60 rupees. This is the only store that sells the Hylian Shield.
Recovery Heart: 1 for 10 rupees.


Name of the Store: Potion Shop
Location: Hyrule Market
Hours: morning/afternoon/evening
Sells:
Blue Fire: 300 rupees. You must have a bottle to keep this in. This is the only store that sells this item.
Bugs: 50 rupees. You must have a bottle to keep this in. This is the only store that sells this item.
Deku Nuts: 5 for 15 rupees.
Fairy's Spirit: 50 rupees. You must have a bottle to keep this in. This is the only store that sells this item.
Fish: 200 rupees. You must have an empty bottle to keep this in.
Green Potion: 30 rupees. You must have an empty bottle to keep this in. This is the only store that sells this item.
Poe: 30 rupees. You must have an empty bottle to keep this in. This is the only store that sells this item.
Red Potion: 30 rupees. You must have an empty bottle to keep this in.


Name of the Store: Bombchu Shop. Once you buy all the Bombchus here, you can't buy any more.
Location: Hyrule Market
Hours: nighttime
Sells:
10 Bombchus: 100 rupees
20 Bombchus: 180 rupees.

Name of the Store: Goron Shop. You need the Goron Bracelet to open the weak wall.
Location: Goron City
Hours: 24 hours a day
Sells:
Bombs: 5 for 25 rupees, 10 for 50 rupees, 20 for 80 rupees, or 30 for 120 rupees. You must have a Bomb Bag.
Goron Tunic: 200 rupees. Young Link cannot buy this. This is the only store that sells the Goron Tunic.
Recovery Heart: 1 for 10 rupees.
Red Potion: 40 rupees. You must have an empty bottle to keep this in.
20 Bombchus: 180 rupees.


Name of the Store: Zora Shop. [[Red Ice]]
Location: Zora Lair
Hours: 24 hours a day
Sells:
Arrows: 10 for 20 rupees, 30 for 60 rupees, or 50 for 90 rupees. You must have the Quiver.
Deku Nuts: 5 for 15 rupees.
Fish: 200 rupees for one. You must have an empty bottle to keep this in. Red Potion: 50 rupees. You must have an empty bottle to keep this in.
Zora Tunic: 300 rupees. Young Link cannot buy this. This is the only store that sells the Zora Tunic. 20 Bombchus: 180 rupees.



=As an adult =

Name of the Store: Bazaar
Location: Kakariko Village
Hours: morning/afternoon/evening
Sells:
Arrows: 10 arrows for 20 rupees, 30 arrows for 60 rupees or 50 arrows for 90 rupees. You need a Quiver.
Bombs: 5 for 35 rupees. You need a Bomb Bag.
Deku Nuts: 5 for 15 rupees.
Deku Stick: 1 for 10 rupees.
Hylian Shield: 80 Rupees. This is the only store that sells the Hylian Shield.
Recovery Heart: 1 for 10 rupees.


Name of the Store: Potion Shop
Location: Hyrule Market
Hours: morning/afternoon/evening
Sells:
Blue Fire: 300 rupees. You must have a bottle to keep this in. This is the only store that sells this item.
Bugs: 50 rupees. You must have a bottle to keep this in. This is the only store that sells this item.
Deku Nuts: 5 for 15 rupees.
Fairy's Spirit: 50 rupees. You must have a bottle to keep this in. This is the only store that sells this item.
Fish: 200 rupees. You must have an empty bottle to keep this in.
Green Potion: 30 rupees. You must have an empty bottle to keep this in. This is the only store that sells this item.
Poe: 30 rupees. You must have an empty bottle to keep this in. This is the only store that sells this item.
Red Potion: 30 rupees. You must have an empty bottle to keep this in. This is the only store that sells this item.


Name of the Store: Goron Shop. You must prove to Darunia's son that you're not Ganon's ally.
Location: Goron City
Hours: 24 hours a day
Sells:
Bombs: 5 for 25 rupees, 10 for 50 rupees, 20 for 80 rupees, or 30 for 120 rupees. You must have a Bomb Bag.
Goron Tunic: 200 rupees. This is the only store that sells the Goron Tunic.
Recovery Heart: 1 for 10 rupees.
Red Potion: 40 rupees. You must have an empty bottle to keep this in.


Name of the Store: Zora Shop. You must melt the red ice with blue fire.
Location: Zora Lair
Hours: 24 hours a day
Sells:
Arrows: 10 for 20 rupees, 30 for 60 rupees, or 50 for 90 rupees. You must have the Quiver.
Deku Nuts: 5 for 15 rupees.
Fish: 200 rupees for one. You must have an empty bottle to keep this in. Red Potion: 50 rupees. You must have an empty bottle to keep this in.
Zora Tunic: 300 rupees. Young Link cannot buy this. This is the only store that sells the Zora Tunic.


Other shops:
Deku Business Scrubs: They're found all over Hyrule, but after getting hit by something, they bribe you with items. Most of these items are very expensive, but there are a few Deku Scrubs that sell shields and pieces of hearts.

Lon Lon Ranch: You can buy Lon Lon Milk from Talon for 30 rupees. You must have an empty bottle, and must be Young Link to purchase it. Lon Lon Milk restores 5 hearts. For a discount, play the Chicken Game.
Potion Lab: When you're Adult Link, go through the path on the left of the Potion Shop's counter to get to the fenced in area. This shop, the Granny's Potion Shop, sells Blue Potions for 300 rupees. This restores both Magic and Health, but you must give her the Odd Mushroom from the Biggoron's Sidequest.
Magic Carpet Shop: Enter the Haunted Wasteland from the Gerudo's Fortress and follow the flags until you reach a sign about the shop. It sells Bombchus for 200 rupees. This is the only Bombchu shop that does not run out of bombchus.