This is a list of theories that have to do wtih both The Legend of Zelda: Ocarina of Time and The Legend of Zelda: A Link to the Past together.
The eye symbol seen on Agahnim's robes in the game's official artwork is supposedly the emblem of Agahnim. In the game, this symbol can be seen on the floor near the sealed entrance to Hyrule Castle Tower and at the entrance to the room in which Agahnim sends the Seven Maidens to the Dark World. This symbol is strangely reminiscent of the Sheikah Emblem. Also in the manga, Legend of Zelda: Ocarina of time-Part 2, Sheik mentions how the Sheikah symbol was originally just an eye and the tear was added after one of the royal families betrayed the Sheikah, which could mean that Agahnim's symbol is the original symbol of the Sheikahs. However, as the game was released before The Legend of Zelda: Ocarina of Time, it could be merely coincidence that the two symbols share similarities. However, in the Temple of Fire in The Legend of Zelda: Phantom Hourglass, the symbol appears on the floor of the boss chamber and in the room outside, implying a connection.
The eye symbol could also have a connection to the "eye" bosses (i.e. Kholdstare, Arrghus, and Vitreous), making it a common theme among Link's enemies in the game. It is not explained why eyes are significant to Agahnim.
Book of MudoraEditWhat appears to be the Book of Mudora has appeared in recent installments of the series. A green book resembling the Book of Mudora is seen on a table in Impa's house in The Legend of Zelda: Ocarina of Time 3D. This house is in Kakariko Village, the same town where the book is found in A Link to the Past. Another identical green book can be found on setting on a chair in theLakeside Laboratory. The only difference between these books and the Book of Mudora in Link to the Past is appearance of Sheikah Symbol on the cover in place of a Triforce symbol. However its possible that these books may simply be a Sheikah edition of the Book of Mudora or that the Book of Mudora was actually based on a more ancient Sheikah text found in both Impa's House and Lakeside Laboratory. It is possible that this ancient Sheikah book were later used by Hyrulean Scholars and/or Sages to create the Book of Mudora or that the Book of Mudora is simply a modern edition of those ancient books.
Princess ZeldaEditThe relationship Zelda has with Link is close, possibly her closest. A popular theory among fans is that of a romantic relationship between some of the Zelda and Link characters in the Zelda series. Although never explicitly confirmed in a video game title, this theory is based on hints given in the games, interviews with the game creators, and content of the animated series, comics, and manga (although the last three are generally considered non-canonical).
One hint of a romance between Zelda and Link is given at the end of The Adventure of Link, when the awakened Princess apparently kisses Link under the falling curtain.
Some cutscenes in Ocarina of Time featuring the two together have been interpreted as signs of an attraction. While Link and Zelda are escaping Ganon's Castle, Zelda will additionally show her concern for Link by shouting out whenever he is hurt. Moreover, in the game's final scene, Zelda and Link are floating in the sky together, sharing a decidedly sentimental (if not necessarily romantic) moment where Zelda apologies for involving Link in the events of the game and seems saddened by the situation. She also stated that she will not forget the time she spent with him in the Child Timeline as shown in Majora's Mask through Link's memory.
In addition, if the Oracle games are played as sequels to each other, the ultimate ending sequence shows Zelda lightly kissing Link on the cheek. Link swoons while hearts float above the pair's heads, and Zelda looks away, blushing. In The Wind Waker, when Zelda is asked to stay in hiding in Hyrule Castle while Link restores power to the Master Sword, she waves goodbye to Link, asking him to be careful.Spirit Tracks features several moments that can be interpreted romantically. Early in the game during the Graduation Ceremony, Zelda walks into the room in front of Link, who is bowing down respectfully. Link then looks up and gasps, blushing at her in amazement. He is then scolded by Chancellor Cole for raising his head without permission. Later, when Zelda's spirit is separated from her body following the first encounter with Chancellor Cole and Byrne, Link is the only one who can see her besides the Lokomos, demonstrating a clear and strong bond between himself and the Princess. After Zelda and Link defeat Byrne in the Tower of Spirits, Byrne, disbelieving, comments that he was beaten by two humans. Zelda, while still possessing a Phantom, says that when she and Link combine their strength, no one can defeat them. Link turns to her, surprised. The background turns white and Zelda's Lullaby plays as they both laugh and high-five, gazing at each other all the while. Toward the end of the game, before the final battle against Malladus, Zelda is reunited with her body, and is no longer able to levitate. Link runs underneath her to catch her as she falls, and she lands on top of him and knocks them both to the ground as well as knock Link out for a few seconds. Upon awakening, Zelda, overjoyed to have her body back, embraces Link, causing him to blush. Finally, after Malladus is defeated, Zelda and Link watch Anjean and Byrne's spirits ascend to the heavens. The camera then lowers to show Zelda and Link holding hands while Zelda's Lullaby plays in the background. After the credits, a short cut scene shows Zelda gazing at a picture of Link on the Spirit Train with her flying beside him, which she keeps on her desk. she may also wave at Link depending on his answer to a question Zelda asked before.
Skyward Sword has several noticeable romantic moments between Link and Zelda. Early in the game, Zelda wants Link to be the first to see her outfit for the Wing Ceremony. She worries over him and she does not want him to fail at becoming a knight. When Link's Crimson Loftwing is hidden by Groose, Zelda assists Link in finding his Loftwing. After Link wins the Wing Ceremony, Zelda jumps off the ledge and Link catches her almost as if she was expecting him to. She then congratulates him on winning. Afterwards, Zelda mentions that she is very happy to be atop the Statue of the Goddess with him. She also gets extremely close to him and almost implies that the two are to kiss, before she pushes him off the statue. Afterward, Zelda bashfully asks Link to go out flying which they do. She then tells Link how amazing the day was, and that she would remember it forever. At the Temple of Hylia, when Zelda states she must seal herself to keep Demise in place, she sheds tears of sadness and states before all this, she was happy just being with Link on Skyloft, demonstrating a deep level of feelings for Link. Link desperately tries to stop her and when she is sealed, Link lowers his head in sadness, showing his deep feelings for her. Much later in the game, when Link releases Zelda from her sealed state, Link runs up and catches her from falling and both of them hug and walk out smiling at each other, holding hands, before Ghirahim ruins the tender moment. During the ending, Zelda asks what Link will do now. Link sweetly smiles at her while their Loftwings fly off toward the sky, implying that he chose to stay on the Surface to live with Zelda.
A Link Between Worlds features some gossip told to Link by the Rumor Guy. He tells Link that one of the castle staff had seen Zelda sneaking off every night. When she followed her, she saw Zelda staring at the painting in Hyrule Castle depicting the Link and Zelda from A Link to the Past cuddling with each other, implying they became more intimate with each other. This also hints the Zelda in A Link Between Worlds wants to have a similar relationship with the Link of her time.
The game creators also seem to be fond of the idea of romance between the characters.
Though never directly stated in-game, Shigeru Miyamoto revealed in an interview conducted by Famimaga 64 that Navi is jealous of Princess Zelda and has feelings for Link.
Another less popular theory among fans is that Link and Zelda are related by blood, either as siblings or more distantly. Even though rumors to this effect started with the infamous "Save the Princess... Zelda is your... ... ..." line from A Link to the Past (later reported as a mistranslation), the theory generally revolves around the Link and Zelda from Ocarina of Time.
A possible indication of a blood relation between the two in Ocarina of Time is their physical resemblance: they both have blonde hair, blue eyes, and similar facial features. They also have similarly shaped heads. Graphics limitations could be responsible for some of this similarity, however. Certain dialogue could also be perceived as implying a blood relation: the ghost Sharp comments that Link reminds him of Zelda, and that Link "may have some connection with the Royal Family". Link's connection to the Royal Family is highlighted throughout the game, with Link often playing Zelda's Lullaby to verify it. The fact that Impa agrees to teach a strange boy a song only Royal Family members are allowed to know could also be interpreted as a hint at Link's blood relation to Hyrule's Royal Family. 
Additionally, Zelda seems to recognize Link's name upon their first meeting. This could be attributed to her prophetic abilities, although the boy in her dreams seemed to be a largely abstract figure, with no defining traits aside from the presence of a guardian Fairy and a Spiritual Stone. This line of dialogue has often been regarded as a sign that the two have met before, although this could only have occurred when Link was a baby per the Deku Tree Sprout's account of Link's coming to Kokiri Forest. It is also worth noting that while the King of Hyrule is clearly identified as Zelda's father, no mention is made of a Queen. Meanwhile, Link's mother is stated to have died shortly after reaching the forest, but no information is given concerning his father. Given these facts, it is possible that Zelda and Link share the same parents, making them siblings.
"In a realm beyond sight the sky shines gold, not blue. There, the Triforce's might makes mortal dreams come true." — Book of Mudora verseThe Sacred Realm (聖地 Seichi?, Sacred Land), also referred to as the Golden Land, is a recurring location in the The Legend of Zelda series. The Sacred Realm is described as a mythical plane, or parallel world, created along with Hyrule by the three Golden Goddesses. It is the resting place of the Triforce, an artifact of great power left by the Goddesses. Though the Sacred Realm is linked to Hyrule, the way to access it and acquire the Triforce within is shrouded in secrecy.
Ocarina of TimeEdit
The backstory of A Link to the Past has many similarities to the events of Ocarina of Time. The name "Seven Wise Men" from A Link to the Past is actually a mistranslation, with the original Japanese and later English re-releases giving them the same name as the Seven Sages from Ocarina of Time. Two of Ocarina of Time's developers, character designer Satoru Takizawa and script director Toru Osawa, even stated that the Imprisoning War and Seven Sages mentioned by A Link to the Past were the same events and characters seen in Ocarina of Time. Despite this, there are some details which conflict between the two accounts. Many fans consider these details to be retconed in the face of overall similarities and developer confirmation, while others maintain that the two games are describing separate events and characters.
The Silent Realm from The Legend of Zelda: Skyward Sword is theorized to be the Sacred Realm. In Skyward Sword, Link obtains all three pieces of the Triforce in a place which appears to be the Silent Realm, given the area's identical appearance, method of entry, and Link's lack of items in the area. Because the stories of the creation of Hyrule state that the Triforce was left in the Sacred Realm, it would make sense that in Skyward Sword, which is generally accepted as the first game in the chronology of the series, the Triforce would be found in the Sacred Realm. The Silent Realm also changes to appear golden upon Link's acquisition of the full Triforce, similar to the Sacred Realm's description as the "Golden Land". However, the nature of the Silent Realm is distinctly different from that of the Sacred Realm. While both are equivalent worlds to Hyrule, the Silent Realm is a spirit world which only Link can enter, leaving Fi, his items, and his own physical body behind. The Sacred Realm, however, is a normal physical world, which any person can enter with their own body and equipment.
Spectacle RockEditSpectacle Rock, located at the summit of Death Mountain, presumably appears as an island on the Great Sea known as Spectacle Island. The Great Sea, the country in which the game is set, was in truth created when Hyrule was flooded by the Gods. Spectacle Rock, the very top of the tall, tall Death Mountain, is the only surviving landmark of that area. However, there is a conflicting theory that Dragon Roost Island is Death Mountain, due to the ring of smoke seen on Link's first visit there and the fact that it is a volcano, as well as the fact that it is taller than all other Islands in the game.
It is speculated by some that alternate worlds such as the Twilight Realm and Termina may be unaffected by the timeline split. However, while these two realms are alternate dimensions, there is no evidence to support the idea that they exist outside of linear time. Both realms have demonstrated the ability to receive beings from the Child Timeline and return them to the Child Timeline when they exit back into Hyrule. There is no reason to believe that these two realms would only exist as a single timeline, or that they could "prioritize" inputs from one timeline, and later output these into both the timelines.
In addition, the renowned Youtube show, Game Theory, dismissed the Zelda Timeline, particularly the Defeat Timeline (in where Link fails on his quest) on the grounds that "the hero cannot be simultaneously victorious and defeated". Elaborating, he explained that with Link defeating Gannondorf, two perfectly possible timelines are created; However if Link dies at any point in his journey another separate timeline is created. Explaining that the only way for all 3 timelines to exist is the Many Worlds Theory (the theory that all possible pasts and futures exist in separate timelines).