In this parody of A Christmas Carol, the Ghost of Christmas Present has the same appearance as Link.
Note that this might be considered an official incarnation of Link, but since he's never recognized and is only called "Ghost of Christmas Present", we consider him only a character based on Link, rather than actually him.
Wario Land II
Some of the game's collectible treasures resemble Zelda items and might be based on them, but may just be coincidences.
Specifically there's an ocarina resembling the flute from The Legend of Zelda: A Link to the Past, a jewel resembling a Rupee, and a winged boot that many think to be based on the Pegasus Boots from the Zelda series, however they were designed with wings only starting with The Legend of Zelda: Four Swords, released after this game, so this is unlikely a reference.
Wario Land 3
March 21, 2000
Once again some of the treasures resemble Zelda items. Specifically there once again are the Pegasus Boots, but still Four Swords wasn't released yet, so they are probably just returning from Mario Land II, and there is a swimfin very much resembling the Zora's Flippers from Zelda games (image on the left), but may once again be a coincidence. Note that there also is what seem to be a hand-flipper.
The Legend of Zelda: Ocarina of Time Master Quest
November 21, 2002
This compilation game includes preview trailers for then-upcoming games published by Nintendo, and among these is a trailer for Wario World.
The Legend of Zelda: The Wind Waker
December 13, 2002
The Armos Knight enemy has a nose and moustache very similar to Wario's. Armos Knights are also featured in some other Zelda games, but this feature is only present in Wind Waker.
Note that this might actually be considered a reference to the Mario series, where Wario originally appeared, but since the game doesn't feature references to any other Mario element, it seems more likely that the creators wanted to reference the hero of the Wario series, rather than a secondary Mario character.
WarioWare, Inc.: Mega Microgame$!
March 21, 2003
One of 9-Volt's microgames is based on The Legend of Zelda.
The goal of the game is to get Link into the cave before time runs out. In Level 2 the game also features the enemy Peahat as an obstacle, while Level 3 features a Peahat and a Zora.
Like all other microgames from the game, this one returns in WarioWare, Inc.: Mega Party Game$!
Additionally, by holding down on the d-pad during the credits, the stars change into the shape of the Triforce. As a side note, by pressing right they change into the GameCube logo. This feature also returns in WarioWare: Touched!
October 14, 2004
One of 9-Volt and 18-Volt's microgames is based on The Legend of Zelda.
The goal is to use Link's shield to deflect attacks by the Red Octorocks before time runs out. Level 1 features only two Octorocks, Level 2 features three Octorocks and Level 3 features a large group of Octorocks, but with only a few of them shooting.
December 2, 2004
9-Volt and 18-Volt's microgame "The Legend of Zelda" is based on The Legend of Zelda and Zelda II.
The object is to tap all fairies onscreen to catch them and restore Link's health before time runs out. Level 1 features only one fairy, Level 2 features two moving fairies and Level 3 features two moving fairies among a group of Like Likes. While Levels 2 and 3 are only based on the first Zelda game, Level 1 is sometimes based on Zelda II.
Additionally, in 9-Volt's "8-Bit Hero" microgame, the player has to find the wrong pixel in a zoomed sprite from a Nintendo game. In Level 3 the image is Link from The Legend of Zelda. After the microgame is won a brief scene from the original game is shown.
WarioWare: Smooth Moves
December 2, 2006
This game features two microgames based on Zelda games, and are both 9-Volt and 18-Volt's microgames:
"The Wind Waker" is based on The Legend of Zelda: The Wind Waker and the goal is to guide Link (holding the Deku Leaf) to land by riding the wind. With higher level, Link will start further away. Its form is "The Mohawk".
"Ocarina of Time" is based on The Legend of Zelda: Ocarina of Time and the goal is to swing the Wii Remote upward to make Young Link pull the Master Sword out of its pedestal in the Temple of Time. With higher level, the sword is harder to pull out. After pulling it out, Young Link will turn into Adult Link in Level 1, into an old Link in Level 2 and into a cucco, the chicken from the Zelda series, in level 3. Its form is "The Janitor".
The game also features some other references to the Zelda series, specifically:
9-Volt and 18-Volt's microgame "Opening Night" features Link playing a violin as one of the musician the player has to conduct. Also, the Zelda theme is one of the songs the orchestra can play in Level 3.
In the game's credits, staff member Ann Lin's Mii appears dressed as Link in the "North American Localization" section. (Ann Lin also did voice acting but her Mii appears in regular clothes in the "Voice Acting" section)
April 29, 2009
9-Volt and 18-Volt's microgame "Zelda" is based on The Legend of Zelda: Phantom Hourglass.
The goal is to defeat all three ChuChus that attack Link by tapping them before time runs out or before one of them touches Link.
Additionally, the Heart, Fairy and Key from The Legend of Zelda are featured as premade objects usable to create original microgames, while The Wind Waker music is one of the unlockable records in the game.
WarioWare: D.I.Y. Showcase
April 29, 2009
18-Volt's microgame "Zelda 2" is based on Zelda II: The Adventure of Link.
The goal is to block all boomerangs tossed at Link by a Goriya, and to do so the player must tap Link to make him stand or crouch.
Copyrights for both series are held by Nintendo.