Deity

Deities are quite common in the Legend of Zelda universe, being present in many games. They are divine figures send by the Goddesses to guide the Hero of Time, among other heroes in the Zelda Universe.

Great Deku Tree

] The Great Deku Tree, as seen in Wind Waker and Ocarina of Time, is seen by most as a deity. He guides the Kokiri, and in Ocarina of Time is the keeper of the Kokiri's Emerald. He also appears to possess much knowledge, as he tells Link of the Golden Goddesses. His power pales in comparison to Ganondorf's, however, as the latter was able to kill him with a curse. The Deku Tree is reborn, however, by the Deku Tree Dprout, who gains all of the Great Deku Tree's knowledge. Therefore, the Deku Tree is semi-immortal.

Jabu-Jabu

Jabu-Jabu is the patron of the Zora in Ocarina of Time, although he appears to have a much lesser role in the Zora community than the Great Deku Tree, as he is seen mostly as a figure. He never speaks to Link, nor does he appear to be the keeper of Zora's Sapphire. In The Wind Waker, however, he is the keeper of Nayru's pearl, and gives it to Link when the King of Red Lions requests it, though he is reluctant to do so It is also unknown how far his power exceeds due to the fact that he disappears after seven years from Zora's Domain, and thus it is possible he has died.

Fierce Deity

The Fierce Deity is the ultimate form Link can take in Majora's Mask. Link can only do this if he obtains all the masks available in Majora's Mask. Due to his brief appearance, much is unknown about the Fierce Deity. It is likely he is related to the moon, as he has a crescent moon emblazoned on his tunic.

Snapper

Snapper is the turtle that takes Link to the Great Bay Temple in Majora's Mask. He appears to be a deity of some sort, as he knows of what is going on in the ocean, and knows of Link's name and quest before he tells him. After Link frees the third Giant, Snapper remarks that he must return to his slumber once more.

Hylia

Hylia is the deity worshipped by the people of Skyloft. She later abandoned her divinity and was reincarnated as a mortal. She also may be the Goddess of Time mentioned in Majora's Mask.

The Giants

Given that the Golden Goddesses have some impact on the goings of Termina, as seen by the Goddesses of Time, coupled with the fact that The Giants actually interact with Link, suggests that they are not gods, but deities.

Theories

There are several indications that Majora was worshiped by the people of Ikana Valley, as there are many symbols in both Ikana Valley and Stone Tower that indicate this.