How can I carry more Rupees, Bombs and Arrows?

Get the Big Wallet, Big Bomb Bag, and Large Quiver upgrades to carry more of each item.

What purpose do the gray stone markers serve?

Examine the marker to turn it into a Wind Crest. You can then use the Ocarina of Wind to teleport to any Wind Crest you have discovered.

Why is Link's outfit a different color?

Whenever you drink one of the Charms, Link will change colors temporarily. His outfit will return to normal when the effect of the Charm wears off.

Is there a way to skip the cut-scene each time Link shrinks?

Yes. Press the R Button to skip the scene.

What do I do with the blue mushroom in Deepwood Shrine?

Pull the mushroom back, then let go of the Control Pad to be thrown forward. Link can use the mushrooms to cross gaps and water.

How do I destroy the spiky turtles in the Cave of Flames?

Let them run into your shield, then hit them with your sword when they are flipped on their backs.

How do I cross the disappearing bridge in the Palace of Winds?

Pull the lever to make the bridge start to appear. Before the bridge has completely reached the ledge where you are standing, face up and dash across with the Pegasus Boots.

In the Temple of  Droplets, how do I push the ice blocks to get the Big Key?

Push the upper block left. Next, push the lower block left, down and left. Push the middle ice block (with the Big Key inside) left, up, left, down, left, up and right.

How do I jump through the stack of clouds in the Palace of Winds?

Stand below the bottom cloud. Hold the button the Roc's Cape is equipped to to jump straight up onto the cloud. Repeat until you reach the top. Be sure that you do not press the Control Pad in any direction when you jump.