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.

Ocarina of Time was originally planned to be played in a first-person perspective, but it was changed to third-person because Miyamoto wanted the change from Young Link to Adult Link to be visible on screen. He also thought players should see Link because "he is so cool looking!"

The twins' house in Kokiri Forest actually has two pots, but the game background only shows one. While technically invisible in-game, Link can still roll in between the two pots, which will result in parts of Link disappearing behind where the second pot should be.

In some trailers of different Alpha/Beta-builds for the game, it can clearly be heard that both Navi and Link had different voice actors. It is also apparent that Navi had different lines of dialogue.

Changing tunics and using certain items while next to a Gerudo warrior can alter the color of the warrior's clothing to match a color value of an item currently equipped to Link.

During beta testing for Ocarina of Time, developers added an Arwing from the Star Fox series to the game to test enemy AI and Z-Targeting. While it was never actually used in the game, the code was never removed and can still be accessed via devices like GameShark and Action Replay.

It's possible to use an empty bottle to reflect Phantom Ganon and Ganondorf's magic blasts back at them, similar to how the Bug-Catching Net can be used to reflect Agahnim's magic in The Legend of Zelda: A Link to the Past. Both items are used in their respective games to catch things, which are then stored in a bottle. Also like the net, there are some advantages to using the bottle: it has a slightly wider swipe and a more consistent motion than the sword.

After killing a Redead, any other Redeads near it will flock around the felled enemy and sit. It's speculated that the Redeads are either mourning the loss of a comrade, or are eating the dead corpse, explaining why it disappears.

The character Sakon can be seen running around the Hyrule Town Marketplace. If the player speaks to him, he will say "Huff huff! I'm late! I'm late! For a very important date!", a quote from the White Rabbit in the novel Alice in Wonderland.

In an early beta version of the game, there was a place known as the "Unicorn Fountain". This was originally going to be where Link was to get the Triforce, and the ability to shoot beams from his sword. It is believed that it was to be accessed through the normally unreachable underwater cave in Zora's Domain.

The game features a crash debugging tool that allowed the developers to find out information as to why the game has crashed. This is still present in all the Nintendo 64 releases, and can be accessed by inputting a series of button combinations after crashing the game. Information about the game and the environment that was present during the crash will be accessible from this screen.

The Version Info screen, however, not only has information about when the game's version was compiled, but also a message which reads, "I LOVE YOU".

Charles Martinet has expressed interest in providing the voice of Link:

The track used for The Legend of Zelda: Ocarina of Time commercials is "Riddle of Steel" from the 1982 film Conan the Barbarian. This same song was also later used for The Legend of Zelda: Twilight Princess E3 2004 trailer.

Link was able to ride Epona into Hyrule Castle Town during later beta-builds of the game. This can be seen in various pre-release trailers. Why it was removed is unknown.

The Plaque that appears in Dodongos Cavern is the exact same one on the fountain in Super Mario 64.

It was originally planned for the Great Fairy to be blue and white. The beta model can be found in the game's data.

In the Hyrule Castle Courtyard, there is a window to the left when you first enter. It's empty, save for a plant. If you take out your slingshot and fire at the plant, it will trigger a guard to appear and say "Hey You! Don't cause any trouble!" then throw bombs at you.

In the Master Quest version of the game, the Water Temple has an extra key that cannot be used. This is due to the fact that a flag in the game's code is accidentally set when Link defeats the three Stalfos in the room with the three dragon heads. This was fixed in the 3DS version.

A time paradox is created in Ocarina of Time. According to Guru Guru in Kakariko Village, Link played the Song of Storms as a child to speed up the windmill, yet Link is taught the song by Guru Guru as an adult. Because of this, the question of who originally composed the song remains a mystery.

Further proof that the Water Medallion was meant to be the Ice Medallion can be found in the fight with the Sorceress Sisters. Kotake's attack symbol (fire) has the same design as the fire medallion and Koume's attack symbol (ice) has the same design as the water medallion.