There is only one crystal left: the one in which Zelda is imprisoned! As the last maiden said, Zelda is within Turtle Rock. That is on the Dark World's Death Mountain. But first...
There is a new type of bomb in the bomb shop, where your house is in the Light World. To get there, warp to the Light World, use your flute to get to your house, go north to the castle gate to get to the Pyramid of Power, and make your way around to the bomb shop.
Inside, next to the pile of ordinary bombs, there is a big pink bomb. You may have noticed a crack in the wall of the Pyramid of Power that you couldn't break open with an ordinary bomb. Well, this Super Bomb will do the trick. Buy it for 100 rupees, and it will follow you until you press A, or drop off a ledge, so be careful not to do that unless you want the bomb to go off! Once you press A or drop off a ledge, the 3 second bomb timer will start, after which the bomb will explode.
To get to the Pyramid of Power quickly, go outside and warp to the Light World, then head north and pass through the castle gate to find yourself right at the pyramid. Walk up the stairs and go to the big crack in the wall. Position the Super Bomb in front of it, then press A and get away. After 3 seconds, the bomb will break open that crack. Go inside.
You find a small pool. As with the Waterfall of Wishing, you can drop things into it, and possibly get better things in return. Approach it, and drop in your bow and arrows, and a fat fairy will appear. She will give you the Silver Arrows, which she says will finish Ganon off!
Before you leave this Mysterious Pond, you should drop in your sword, too. The Fat Fairy gives you the Golden Sword, twice as powerful as the Tempered Sword!
If, for some reason, you used your green potion, you can also throw an empty bottle in and she fills it with green potion, just like in the Waterfall of Wishing. You will really need the green potion in the next dungeon, so if you want you can even empty a second bottle and have it filled with green potion, too.
If you're ready, warp to the Light World, use your flute to get to #1, Death Mountain, and climb to the Dark World warp tile at the top. Warp there, then use the Magic Mirror to get on top of Spectacle Rock. Drop down from there and head east past the Tower of Hera to the next screen. Cross the bridge, pounding down a post, and ignoring the cave entrances to go east to the next screen. Lift the black boulder below. You must now pound the posts up here in the correct order. First pound the one on the right, then the one above, and finally the one on the left. A warp tile will appear. Step on it to enter the Dark World.
You find yourself atop a rock that looks like a turtle; Turtle Rock! Below you is a wavy symbol on the ground that may look familiar. Look in your inventory and you see that symbol on the Quake Medallion. Stand on the symbol and use the medallion, and the turtle's head will vanish, revealing stairs that lead into the dungeon.
Don't go in yet! There is a piece of heart (the second-to-last one) that you can now get, though it is a bit tricky. Drop down from atop Turtle Rock and exit west. Pick up the white boulder below and go down the stairs. There are many platforms here, some with chests. They all just contain rupees, and your wallet should be full by now, so you can ignore them. Head north up the path until it ends. There is actually an invisible path north of you. If you use the Ether Medallion, the path will be illuminated briefly, but that uses up so much magic it's really a waste (and you may not remember the exact path, anyway). Another way to cross the path is to create an orange block with the Cane of Somaria, and push it forward (SLOWLY) along the invisible path until it falls off the edge. Now you know you need to turn in another direction. Face east and create another block. Push it until it falls. The next turn is north, then west, then you have a straight shot north so you don't need to create a block. Bomb the north wall, then in the next room bomb the west wall. (The north wall just leads to a fairy fountain, and the east wall can't be bombed.) Exit west (the north wall just leads to a few fairies floating around), then exit south to the outside. Use the Magic Mirror to get back to the Light World, where a piece of heart will be sitting right there waiting for you.
Step back into the warp you created, then drop off the edge to get back down to the path that lets you reach Turtle Rock. Go east back to Turtle Rock. (By the way, you can pull the right-hand paw for 20 rupees.) Enter the dungeon...