The Legend of Zelda: The Wind Waker

The first Zelda for the GameCube in 2002 (2003 outside of Japan) met with mixed reviews. While the gameplay and story were largely praised, there were complaints about the graphical style and the amount of time spent traveling through the enormous world. The cartoony, cel-shaded animation and bright colors lent Wind Waker the appearance of a childlike game which turned off adults who had grown with the series, and it took some time to come to terms with the surprisingly dark storyline behind the cheerful exterior. The name of the game—as well as its musical theme—comes from a conductor's baton that has power over the wind and, among other purposes, is instrumental in your ability to travel.

Many, many years after Ocarina of Time, the world is now a far-flung mass of islands separated by huge swathes of ocean. Link is a boy who's grown up on an island that tells the legend of the Hero of Time and who dress their boys in green when they come of age in order to inspire them with the ancient Hero's courage. When the day comes for Link to receive his green clothing, a giant bird kidnaps his sister, Aryll. With the help of the pirate girl, Tetra, Link gives chase and finds that Ganon has been kidnapping girls in an attempt to find Zelda. Overpowered, Link embarks on a massive quest to find the Master Sword once used by the Hero of Time, restore it to its former power, defeat Ganon, and save the world.

Images:

Link and Aryll
A sad Link waves goodbye while Tetra waits
Phantom Ganon
Plowing the waves
Conducting the wind
Slinking along a cliff face
A rather grainy Zelda

The Legend of Zelda: Majora's Mask

In a rare move, a direct sequel to Ocarina of Time was released in 2000. In an even rarer move, a Zelda game was issued without a Zelda. Featuring the same Link and Epona from its predecessor, everything else is changed when they inadvertently ride into a parallel world. There are three major aspects to Majora's Mask: time, music, and masks. Unlike Ocarina's time travel, Mask relies on a constant timer and a fixed three-day period. Many of the songs from Ocarina are reused, as well as a number of new ones. Masks, which were a small side-quest in Ocarina, take the forefront in Mask (as evidenced by the title) allowing you to perform special tasks, enhance abilities, and even change form by wearing them.

Link is at a loss following his previous exploits. While wandering in the forest he's accosted and loses his horse. After chasing down the thief he's transformed by magic and left, stranded, in a strange, alternate reality. In return for help in resuming his human form, Link agrees to retrieve Majora's Mask for a traveling mask salesman, an ancient and powerful artifact that was stolen by the same person that attacked Link. There's only three days until the Masked thief calls the moon out of its orbit, so the race is on!

Images:

Deku Link is baffled
Goron Link is massive
Jamming with Zora Link
Transforming has a price
Very scary Oni Link—as a collectible figurine!
The opening movie and very early gameplay