This humorous manga starts with Samus in her Gunship playing The Legend of Zelda on her ship during the trip to Zebes.
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 Metroid Prime.
Since the footage comes from a beta version of the game, it shows a fight with a Cloaked Drone using the X-Ray Visor, which should be impossible to get that early in the game.
Metroid Prime 3: Corruption
August 27, 2007
If the Ship Bumper Stickers are unlocked, then stickers will appear on Samus' Gunship depending on what save data the player has on their Wii.
A savefile for The Legend of Zelda: Twilight Princess will make the Royal Crest of Hyrule appear on the ship.
See here for other available stickers.
Copyrights for both series are held by Nintendo.