The Great Deku Tree is considered the 'Father of the Forest', and his first appearance is in Ocarina of Time. In it, he is charged with watching over the Kokiri, a child-like race of forest spirits that live in the Kokiri Forest. He is an exceptionally large tree with a humanoid face and big mustache.
When Ocarina of Time begins, the Great Deku Tree is suffering from a curse cast upon him by Ganondorf in an effort to gain the Spiritual Stone of the Forest, which is in the Deku Tree's possession. Knowing Link's destiny, the Deku Tree sends Navi the fairy to retrieve the boy (who is, at this time, living among the Kokiri as one of them) and asks him to destroy the cause of the curse, a spider called Queen Gohma, within him. Although Link defeats Queen Gohma, the Deku Tree was doomed before Link had begun; before he dies, the Deku Tree gives Link the Kokiri Emerald and tells him to seek Princess Zelda at Hyrule Castle. After adult Link completes the Forest Temple and returns to the site of the Deku Tree, he discovers a little sprout, which grows into the Deku Sprout. It is this sprout who tells Link the truth about his past, and reveals that Link is not a Kokiri, but rather a Hylian who was entrusted to the Deku Tree by his mother, who died soon after.
In The Wind Waker, the Great Deku Tree is the guardian of Forest Haven and is a legendary forest and earth spirit. He is at first plagued by ChuChus and, after Link assists in removing the ChuChus, the Deku Tree tells Link about Forest Haven and the Koroks who live there. He confesses to Link that his energy is actually waning and that he has become feeble with age. It is assumed that this is the same Deku Tree that was a sprout in Ocarina of Time, as he speaks Hylian and remembers old times when he sees Link's green tunic. He gives Link the Deku Leaf to help him on his quest, and later Farore's Pearl after Link rescues Makar from the Forbidden Woods. Like Valoo and Jabun, he speaks Hylian, but he can also speak the modern language of the Great Sea.
The Great Deku Tree and its Sprout also appear in Freshly-Picked Tingle's Rosy Rupeeland.
Source: Wikipedia, "Characters in The Legend of Zelda series," available under the CC-BY-SA License.