In the Hyrule Castle courtyard, in one of the windows you can see pictures of Mario, Luigi, Yoshi, Peach and Bowser. In Ocarina of Time 3D, the pictures were replaced with a Mario level background with warp pipes and blocks.

The sound of the warp whistle from Super Mario Bros. 3 (which uses the same sound as the recorder from The Legend of Zelda) can be heard in the title theme.

At the bottom of the pool inside the Lakeside Laboratory is a motionless shark behind a set of bars.

The characters Talon and Ingo are loosely based on Mario and Luigi.

At the fishing hole, if you cast your line just right, you can catch the shop owner's hat, revealing a bald patch on his head.

Malon wears a brooch in the shape of Bowser's head.

Although Majora's Mask is a direct sequel to Ocarina of Time, there was an official novel released set shortly after the events in the game. "Link and the Portal of Doom" was written by Tracey West and published by Scholastic in 2006 as part of the Nintendo Heroes series.

In the book, a mysterious portal suddenly appears in Hyrule which absorbs all things around it and threatens to destroy the land. Link and Navi have to travel across Hyrule to learn five parts of a song which will destroy the portal.

Although officially licensed by Nintendo, it's considered to be non-canon.

After acquiring the three Spiritual Stones and obtaining the Ocarina of Time from Zelda, if players head straight to the Back Alley of Hyrule Castle Town, they'll find a fatally wounded Soldier. If players talk to him, he'll tell how Ganondorf betrayed the King and that he was injured trying to fight Ganondorf's men so Zelda and Impa could flee. He tells Link to head to the Temple of Time and dies soon after.

If players try to talk to him again, a message will appear saying "He's not moving anymore...."

The Iron Knuckles enemies are actually Gerudo Thieves in armor. Removing the chest plate reveals a curvy feminine figure, and since the Gerudo are all female it seems that this was intentional, and Nintendo didn't just aimlessly use them as a base.

In the German version, the carpenters are named John, Paul, George & Ringo, after the 60's British pop group The Beatles.

When starting development on Ocarina of Time, Nintendo weren't sure how large of a game they'd be able to make with the Nintendo 64's memory restrictions. Miyamoto even considered structuring the game in a similar fashion to Super Mario 64, with Ganon's castle being the hub. The Forest Temple with Ganon's doppelganger jumping in and out of paintings was an idea carried over from that period of development.

After slashing a sign with your sword in Ocarina of Time, playing Zelda's Lullaby while near the sign will repair it. Once the song is finished, the solving a puzzle jingle plays and the sign magically repairs itself.

This same thing happens in Majora's Mask with playing the Song of Healing.

It's speculated that the forest and water temples in Ocarina of Time were originally wind and ice temples. The symbol on the Water Medallion from the Water Temple appears to have a snowflake on it, and the Forest Medallion design resembles a fan. This connection is further supported by the interior of Ganon's Tower, which is based on different temples. The Forest Temple portion of the tower has a wind puzzle based around fans, and the Water Temple portion of the tower is based on ice.

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.

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.