From ANN:
After a new evil is released, Link draws the Four Sword and is split into four. Along with three other Links, he travels through Hyrule, rescuing each of the seven maidens that have been captured by Gufuu. Although they aren't very fond of the idea, the four Links must learn to work together in order to destroy their new foe.

From AnimeCouncil2:

The Legend of Zelda: The Wind Waker - Link's Logbook is a record of Link's journey. On his travels he meets many unique people, and gets into many different varieties of trouble before finally confronting his destiny.

Based on the Gameboy Advance game

Link, a shepherd from Ordon Village, sees village children, including with his childhood friend Ilia, being kidnapped by monsters. He chases after them only to find his world covered in twilight. Thereupon Link suddenly transforms into a wolf and finds a mysterious character named Midna. His journey to bring back light into the world begins.

(Source: MU)

The Black and White arc of Pokemon Special.

(Pokemon Special has several different arcs serialized in parallel in a few different magazines, so the exact numbering for the BW arc is unknown. Hence, this is registered under a completely new series)

The Super Metroid comics, drawn and written by Benimaru Itoh, were released in Nintendo Power issues 57 to 61 in the summer of 1994. They contain a highly paraphrased version of the game's storyline, and the introduction of new characters such as Old Bird, Chairman Keaton and Armstrong Houston.

A Super Mario Collection (AKA Super Mario All-Stars) Guidebook that features a few 4koma gag strips scattered throughout, containing some fun interpretations of the games in the collection clashing, or metatextual comparisons between “then” (the 80s) and “now” (the 90s).

"Ness' Great Adventure, a manga comic that closely follows the story of Mother 2, in the comic, like Mother 2 it includes weird humor and interesting uses for items much like the "Help!" description option in Mother 2. Added in this comic are discussions between Itoi, Itoh (the guy who drew this manga, and also did the character design in Mother 2) and Kohichi Ohyama (Art Director), who talk about what the actual meaning of "Mother" is, and other stuff." - from Starmen.net

Star Fox is the name of a 132-page series of comic pages that ran in Nintendo Power in eleven 12-page installments from February 1993 until December 1993.
It is an adaptation of Star Fox for Super Nintendo, with an early expanded plot that is noticeably different from subsequent installments.

A 2 volume manga that explores the origins of Samus Aran.