Goddess Pearl

The Goddess Pearls were used in The Wind Waker to open up a passage to the Tower of the Gods, which was underwater in sunken Hyrule. Once collected, the pearls were placed on the three Triangle Islands 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 one of three pearls that Link has to obtain in The Wind Waker. 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.

Din's PEarl has the same mark on it as the symbol for the Tune of Currents from Oracle of Ages and as the Power Gems from Phantom Hourglass. This symbol also appears on a door in the Temple of the Ocean King, but the Spirit of Power is needed to open it.

Farore's Pearl
Farore's Pearl is one of the pearls that is obtained by Link in The Wind Waker, being kept by the Great Deku Tree in the Forest Haven. It was going to be given to Link after the Kokork's annual ceremony, until Linder flew 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.

Farore's Pearl has the same mark on it as the symbol for the Tune of Echoes from The Legend of Zelda: Oracle of Ages|Oracle of Ages and as the Courage Gems from Phantom Hourglass. The same symbol also appears on a door inside the Temple of the Ocean King.

Nayru's Pearl
Nayru's Pearl is one of three pearls that Link has to obtain in The Wind Waker. This pearl was 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.

Nayru's Pearl has the same mark on it as the symbol for the Tune of Ages from Oracle of Ages and as the Wisdom Gem.

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

 * 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.