Goddess Pearl

The Goddess Pearls are three major Quest Items that appear in The Wind Waker. Each of them bear their respective marks of the goddesses.

Quest Purpose
The sacred pearls are used to open up a passage to the Tower of the Gods, which lies underwater in sunken Hyrule. Once collected, the pearls are placed on the three statues resembling the Golden Goddesses located in each of the Triangle Islands found across the Great Sea to cause the temple to rise above the sea. The pearls were named after the goddesses Din, Nayru, and Farore.

Din's Pearl
Din's Pearl is the first of three pearls that Link has to obtain. This pearl is Prince Komali's precious possession, as it was given to him by his deceased grandmother. Komali wanted to visit Valoo and get the scale needed to grow his wings; however, Valoo was acting up at the time, making Komali feel upset. Link, with aid from Medli, manages to defeat Gohma and calm Valoo down. Prince Komali feels that giving the pearl to Link would give him courage, and thus decides to give it to Link. Later on, Link places the pearl on Northern Triangle Island to make the Tower of the Gods rise from the Great Sea.

Farore's Pearl
Farore's Pearl is the second of the pearls that is obtained by Link in The Wind Waker, being kept by the Great Deku Tree in the Forest Haven. It is initially going to be given to Link after the Korok's annual ceremony, until Linder flies in, crying that Makar had fallen into the Forbidden Forest. After Link rescues Makar, the Great Deku Tree bestows Farore's Pearl upon the young hero. Link later on places the pearl on Eastern Triangle Island to raise the Tower of the Gods out of the Great Sea.

Nayru's Pearl
Nayru's Pearl is the third and last of three pearls that Link has to obtain in The Wind Waker. This pearl is initially owned by Jabun of Greatfish Isle. However, when Link travels to the isle, he finds that it has been destroyed by Ganondorf. Fortunately, Jabun sensed him coming and fled to Outset Island. Link and the King of Red Lions travel to his cave after the stone door is broken down by Link using the cannon and bombs. Jabun, after some convincing from the King of Red Lions, then gives the pearl to Link. Link then places the pearl on Southern Triangle Island to raise the Tower of the Gods from beneath the Great Sea.

Theory
Some have noted the similarities shared by the Pendants of Virtue, the Goddess Pearls, the Spiritual Stones, and the Elements. This could indicate a direct link between these artifacts, or equally it could simply be an example of the designers' desire to create a feeling of familiarity or a sense of a "shared legend" within the series.

Trivia

 * The Spirit Gems in the game, Phantom Hourglass, look exactly the same as the Goddess Pearls.
 * In Oracle of Ages the symbols of the Tune of Currents, Tune of Echoes, and Tune of Ages look respectively similar to the symbols on Din's Pearl, Farore's Pearl, and Nayru's Pearl.
 * The symbol on Nayru's pearl bears resemblance to the Zora's Sapphire.
 * The symbol on Din's Pearl is found on the banners in Clock Town in Majora's Mask.