The Gloomy Galleon level music in Donkey Kong 64 originates from Dream: Land of Giants, the game that eventually became Banjo-Kazooie. Fittingly enough, it was originally intended to be the theme for Captain Blackeye, Dream's villainous pirate antagonist, who would later go on to cameo as a non-playable character in Banjo-Tooie's Jolly Roger's Lagoon world.

As a bonus feature for Rare Replay, Rare included a set of music tracks dubbed "Top-Secret Tunes", which primarily features previously unreleased music from Rare games in development, including many hailing from Dream. One of these is a rendition of Blackeye's theme, called "High Tides, Swift Sails". While Rare had made efforts to avoid any legal issues with Nintendo as they were putting together Rare Replay (such as removing the remix of the Donkey Kong Land boss battle from its version of Blast Corps), this song's appearance may be an exception as the original version comes from a game owned by Rare that was never completed, while the game the song was repurposed for was never planned to be included in Rare Replay to begin with.

GoldenEye 007 was originally planned to be included in Rare Replay, even going so far as having two "Rare Revealed" documentary videos produced that focused on the making of the game and cut content, but was scrapped due to licensing issues. These videos would later be leaked online in 2019 by a former Rare employee, and the game would eventually be re-released separately in 2023, with owners of the digital release of Rare Replay being gifted the game free of charge.

Because the game is themed around musical-style theater, three types of songs were originally considered for the game's opening number. The first was based on the concept of the "I Want Song", a type of song in musical theater involving the characters singing about the key motivating desire that will propel everyone (including the audience) through the remainder of the show. The second song involved the characters singing what they would do if they were in the same place together. The third type of song that was actually used in the game involves the characters singing about the game in a narrative-style chorus.

Out of all the games featured in Rare Replay, Grabbed by the Ghoulies was the only one to be remastered to run natively on the Xbox One, while other games received only bug fixes and minor adjustments to their controls.