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 had to be placed on the three Triangle Isles 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 had to obtain in The Wind Waker. This pearl was owned by Prince Komali, given to him by his deseased grandmother. However, Valoo had been acting up lately, so Prince Komali felt sad and wouldn't give it to Link, since Komali wanted to go and visit Valoo to get the scale needed to grow his wings. However, Link and Medli managed to defeat Gohma and calm Valoo down. Giving the pearl to Link would give Komali courage so he gave it to him. Link placed the pearl on Northern Triangle Island to make the Tower of the Gods rise from the Great Sea. It 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.
Farore's Pearl
Farore's Pearl is one of the pearls that Link obtained in The Wind Waker. It was owned by the Great Deku Tree and he was going to give it to Link, but then Linder came in, saying that Makar fell into the Forbidden Forest. However, Link rescued Makar and got the Pearl. Link placed the pearl on Eastern Triangle Island to raise the Tower of the Gods out of the Great Sea. It has the same mark on it as the symbol for the Tune of Echoes from Oracle of Ages and as the Courage Gems from Phantom Hourglass.
Nayru's Pearl
Nayru's Pearl is of three pearls that Link has to obtain in The Wind Waker. This pearl was owned by Jabun of Greatfish Isle. However, Ganondorf wanted it and went to destroy Greatfish Isle. Fortunately, Jabun sensed him coming and fled to Outset Island. Later, Link and the King of Red Lions came into his cave. Jabun then gave the pearl to Link. Link placed the pearl on Southern Triangle Island to raise the Tower of the Gods from the Great Sea. It has the same mark on it as the symbol for the Tune of Ages from Oracle of Ages and as the Wisdom Gems from Phantom Hourglass. This part of the quest for the pearls is considered the easiest, as it is the only one that does not require beating a dungeon to get.
Theory
Some have noted the similarities shared by the Pendants of Virtue, the Goddess Pearls and the Spiritual Stones. 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.