Great Deku Tree

Ocarina of Time
The Deku Tree made his first appearance in Ocarina of Time as guardian of the Kokiri and of their forest. He protects the Kokiri's Emerald, one of the three Spiritual Stones.

The Great Deku was cursed by Ganondorf in Ocarina of Time, and embarked Link on a quest to save Hyrule. He died shortly after telling Link to go save Princess Zelda. When he died, a seed fell from one of his higher branches to the ground. As an adult, Link goes back to find a new Deku Tree Sprout growing in front of the old Deku Tree. The Great Deku Tree tells Link the story of the three golden goddesses, and how Hyrule and the Triforce were created.

It is possible that the Deku Tree became the Forest Temple of Twilight Princess, seeing its striking similarities to the appearance of the Temple.

Deku Tree Sprout
The Deku Tree sprout is the successor to the Great Deku Tree as the protector of the Kokiri Forest and, by extension, Hyrule itself. He appears in Ocarina of Time after Link has defeated Phantom Ganon and received the Forest Medallion from Saria with the words, "Hi there! I'm the Deku Tree sprout!" He tells Link the story of how he ended up in the care of the Great Deku Tree, then urges him to complete his quest and defeat Ganondorf.

The Wind Waker
One thing that set the Deku Tree of the Great Sea apart from his predecessor was that each year, the Great Deku Tree would send off some of the Koroks to plant trees all throughout the islands. This was done in the hope that, as the forests spread and the trees grew, they would consolidate the remaining land above the Great Sea, and allow some of the land lost during the Great Flood to be reclaimed from the depths. It also rejuvenates his power.

Freshly-Picked Tingle's Rosy Rupeeland
The story of the Great Deku Tree in Freshly-Picked Tingle's Rosy Rupeeland is somewhat similar to that of the one from Ocarina of Time. Due to pollution, the Deku Tree Sprout is dying, while at the same time the Great Deku Tree is also nearing his end. When Tingle met them, the Great Deku Tree asked if he would enter him and retrieve forest water, which could cure the Deku Tree Sprout. Tingle accepted and entered the Deku Temple. After defeating Bana Bana, Tingle could get the water and rushed back to cure the Deku Tree Sprout. After that, the Great Deku Tree died, happy, and not before paying Tingle for his service.

Parallels

 * In Holodrum, there is no Deku Tree, instead it is replaced by the Maku Tree
 * In Labrynna, there is no Deku Tree, instead it is replaced by the Maku Tree

Manga

 * In the manga version, there is another talking tree known as the Bagu Tree. He lives in the Lost Woods and has never beaten the Great Deku Tree once. The rumor that if you get lost in the woods, you turn into a Skull Kid is true, as that is what the Bagu Tree does to them. He is later killed.
 * The manga also depicts a Gossip Stone, which says the Deku Tree is troubled that he cannot scratch his own back.