The House That Gave Sucky Treats
October 27, 2001
In this Homestar Runner Halloween cartoon, the various charactars from the series trick-or-treat the viewer, and he or she can choose what candy to give them. When The Poopsmith and Pom Pom show up, instead of giving them one of the three possible candies, the viewer can choose to give them the Pumpkin that's lying on the floor. This will play the "puzzle solved" jingle from the Zelda series, and unlock Homsar as the next Trick-or-Treater.
Strong Bad Email japanese cartoon
January 06, 2003
At the end of Strong Bad's 57th email, the viewer can click on the words "Japanese cartoons" on Strong Bad's screen to access an easter egg. After clicking a second time, a different easter egg clip is accessed, showing Homestar Runner watching a TV screen. Below the screen there are some video tapes, including one labeled "NES endings". By clicking on it, a window pops up showing a scene from the ending of a NES game, taken as a picture of the TV screen. By clicking on the window, the viewer can change game, and one of them is the ending to The Legend of Zelda.
November 01, 2005
In this Homestar Runner Halloween cartoon, Homsar appears dressed as Tingle from the Zelda series. He's floating on a balloon and also throws confetti like the original character. One of the fake possible choices for the player to click also reads "That's a lot! A lot! A lot! A lot!" which is a quote by the banker from Majora's Mask, spoken whenever the player deposits between 10 and 99 Rupees at once.
Like in most of his appearances, Homsar is only found as an easter egg, specifically he's met if the viewer clicked on The Poopsmith in the previous scene.
Why Come Only One Girl?
October 27, 2006
This Homestar Runner video exclusive to the DVD "Everything Else, Volume 2", explains why Marzipan is the only main female character in the series, by showing many scrapped ideas for other girl characters. A character nicknamed "The Hurricane" is explained to be scrapped because the creators were distracted by a new Zelda game coming out. As they say so, she disappears in front of Marzipan and Homestar Runner, to which he responds: "Why, Ganondorf?! Why?!" Then he suddenly takes a small bottle and swipes Marzipan into it, just like Link does with fairies in the Zelda series. The item collected music is also heard, and the message "You caught a Marzipan!" flashes on screen.
Strong Bad Email the chair
(December 04, 2006)
Strong Bad's 162nd email is about him getting a new chair. Having a large seatback, it covers most of the scene, and Strong Bad happens to show two of the series's most discussed secrets: what he looks like under his mask, by removing it, and what his parents look like, by showing a picture of them. In the actual video only a small part of the picture can be seen, but decompiling the flash file for the episode the actual image has been uncovered, and it only shows the message "nice try dodongo!"
Dodongos are common enemies from the Zelda series.
Note that this counts as an unreleased link, since the reference is only in the flash file, not the episode itself.
Strong Bad Email unnatural
February 05, 2007
Strong Bad's 166th email shows a giant Bubs attacking Strong Badia, and he's called "King Bubsgonzola Supreme". His introduction, with a closeup and name display, is based on the introduction of bosses in 3D Zelda games, as revealed in the DVD commentary for the episode.
August 03, 2009
This Homestar Runner cartoon begins with the Poopsmith putting a letter into Strong Bad's mailbox, and he appears dressed as the postman from the Zelda series, only with the bunny logo on his hat and shirt replaced by an image of The Cheat.
Doomy Tales of the Macabre
October 29, 2009
In this Homestar Runner Halloween cartoon, The Poopsmith appears dressed as Darunia from The Legend of Zelda: Ocarina of Time, and Strong Bad is dressed as the Skull Kid from Majora's Mask, wearing the titular mask.
Clicking on The Poopsmith at the end of the video will make him dance as Homestar sings "Saria's Song", referencing the scene in Ocarina of Time where Link plays that song to Darunia. Notably, in this final scene Darunia is miscalled "Goron King Dirunia". In addition to the spelling error, Darunia (though the leader of the Gorons) is not a king.
Clicking on Strong Bad will make a face appear on the Moon, and he'll say "Oh no, the evil moon is crashing into the Earth again! What a totally un-frustrating way to play a video game!" this references the plot of Majora's Mask, where the Moon would fall down after 3 days, and Strong Bad's comment on frustration references how in the game the player has to travel back in time many times causing frustration among some gamers having to repeat similar parts of the game frequently. The face on the moon also resembles the one in the game very much.
The creators of Homestar Runner held no right over Nintendo's Zelda, but they only included minor references to the series.