In Metal Gear Solid 4, the opening drum beats from "Snake Eater" will sometimes play when the player equips the Patriot. The full song itself is also used as the music for the third phase of the Final Battle between Solid Snake and Liquid Ocelot on top of Outer Haven. It can be unlocked as an iPod song by collecting all emblems, and will give gameplay bonuses when played during combat.
A piano version of the song is played in Metal Gear Solid: Peace Walker during flashbacks relating to The Boss as well as during both instances where Big Boss attempts to remove the memory drives. It is an unlockable song for the Walkman.
A cover version performed by Donna Burke is featured in the soundtrack Metal Gear Solid ~Vocal Tracks~.
"Snake Eater" is also available as a collectible cassette tape in Metal Gear Solid V: The Phantom Pain, found at Outpost 21 in the Angola-Zaire border region. In addition, the song, or rather, the variant used for the final five minutes of the battle against The Boss in Metal Gear Solid 3, will also be made available for BGM in the version 1.02 update for Metal Gear Online 3, titled "MGS3 THE BOSS."