The Legend of Zelda: Ocarina of Time
(November 21, 1998)
An Airwing from the Star Fox series is present in the game's code, though it's unused. It's unknown what its purpose originally was, but it was likely either used as a placeholder during beta testing, or it's the leftover of a scrapped easter egg. By hacking it was revealed that it's met in Kokiri Forest and is treated as an enemy. It also flies around and attacks by shooting, unlike any other enemy in the game. After being defeated, it crashes on the ground.
The Legend of Zelda: Majora's Mask
April 27, 2000
In the mask subscreen of the game there are five collectable masks based on animals on the same row, and are, in order, Keaton Mask (fox), Bremen Mask (bird), Bunny Hood (rabbit), Don Gero's Mask (frog), and the Mask of Scents (pig). This corresponds to the species of the members of the Star Fox team, in order of importance: Fox McCloud, Falco Lombardi, Peppy Hare, Slippy Toad, and Pigma Dengar. This however was never actually confirmed to be a reference, and is believed by some to be a coincidence.
Copyrights for both series are held by Nintendo.