What is there to spend my rupees on?

I would say that the Pond of Happiness is a good place to spend rupees. You can find the pond inside a cave on an island in the middle of Lake Hylia. You will need to buy Zora Flippers from Zora in Zora's Lake for 500 rupees in order to swim to reach the island.

Depositing 100 rupees allows the player to increase their bombs or arrows carrying capacity by 5 for each 100 rupees deposited. You can do this up to a maximum of 50 bombs and 70 arrows (with the last upgrade for each being an increase of 10).

It looks like you can only throw in either 5 or 20 at a time, unless you have met Venus, in which case, it is 25 or 50.

At first, Link can only throw in 5 or 20 Rupees at a time. After he meets Venus, the amounts increase to 25 and 50 Rupees.

Besides this, there is no way to increase the carrying amount of how many rupees you can hold. It's only 999 for a Link to the Past.

Blue Potions, 160 - 640 Rupees

When you get to the later dungeons, You'll want to stock up on potions, and a lot of them. Both magic and health can run low as the difficulty increase. You can get 4 jars for holding potions. There is a magic shop close to Zora's waterfalls, where you can get three kinds:

• Blue Potion - 160 Rupees
• Green Potion - 60 Rupees
• Red Potion - 120 Rupees

refilling four jars with blue potions will cost you 640 rupees, and at this point in the game, you might use them fast, and not have as many richly filled treasure chests available for plundering.

Full guide to Shop Costs and Shop Locations.

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Shop Costs:

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Rupee costs for 100% items:

Bottle costs 100 rupees.

Flippers cost 500 rupees.

Kiki first asks for 10 rupees to follow you, and then 100 rupees to open PoD.

The capacity-upgrading faerie requires 800 rupees to max out bombs, and 800 rupees to max out arrows.

Potion shop:

Red Potion: 120 Rupees

Green Potion: 60 Rupees

Blue Potion: 160 Rupees

Light World shop:

Red Potion: 150 Rupees

Single Heart: 10 Rupees

10 Bombs: 50 Rupees

Dark World shop:

10 Arrows: 30 Rupees

Bee: 10 Rupees

Fire Shield: 500 Rupees

Dark world Bomb Shop:

30 Bombs: 100 Rupees

SuperBomb: 100 Rupees (Only after getting crystals 5 and 6 (Ice Palace and Misery Mire))

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Shop Locations:

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Bottle:

Bought from merchant in Kakariko Village

Flippers:

Bought from the Big Zora (Top right of map, Light World)

Kiki:

In the Dark World Hedge Maze (Right side of map)

Capacity-upgrading faerie:

In the middle of Lake Hylia (Bottom Right of map, Light World)

Potion Shop: Flute warp #2, between Zora Waterfall and Eastern Palace

Light World Shops:

In Kakariko Village, Small house in the south

Eastern Death Mountain

Lake Hylia North Cave

Dark World Shop:

Thieves Town

Dark World Bomb Shop:

Dark world equivalent of Link's House