Kaepora Gaebora, the large owl who supports and informs Link throughout his adventure, has been confirmed to be the physical form of Rauru, the Sage of Light. Link meets Rauru in the Chamber of the Sages, the first time when he pulls out the Master Sword in the Temple of Time. According to the series' lore, Rauru built the Temple of Time and remained inside the Chamber of the Sages to protect the Triforce, with the owl as his way to communicate with the outside world. Headmaster Gaepora from The Legend of Zelda: Skyward Sword (2011) is rumored to be a direct ancestor of Rauru (as both men look very alike and are very knowledgeable).
Malon's brooch is a Bowser head.
Link's fairy Navi has been voted as one of the most annoying game characters of all time by such media as GamesRadar, Cracked and Nintendo Power. Her recurring line "Hey! Listen!" even became a popular meme that emphasized the character's habit of constantly interrupting the gameplay.
In the German version of Ocarina of Time, if you speak to Princess Zelda while wearing the Keaton mask, she will say:
"Was bist du denn? Ach, du bist eines dieser goldigen kleinen Taschenmonster, oder?"
Which roughly translates into:
"What are you? Oh, you're one of those golden little pocket monsters, right?"
Referencing the visual similarities between the mask and Pikachu.
Hyrule field serves as the game's traditional 'overworld', linking all dungeons and smaller areas together. Since the game designers weren't sure whether such a large 3D area could be realized within the Nintendo 64 system, they had designed a back-up in the form of a castle with paintings. This castle would serve as a central hub from which Link could travel to other areas via the paintings (similar to Super Mario 64). This turned out to be unnecessary when Hyrule field proved to be possible, so the castle was reused as the dungeon called 'Ganondorf's Castle'; the paintings idea was reused for Link's battle with Ganondorf's spirit in the Forest Temple dungeon.