A reversed example: in the combined game, when you play Launch Base Zone (the final level of Sonic 3) as Sonic or Tails, the game skips over the original final boss of the level ( including the awesome ending music).
Much of Knuckles' content for the original Sonic 3 zones is present in the Sonic 3 cartridge, but can't be accessed without attaching it to the Sonic & Knuckles cartridge.
Sonic 3 Limited Edition, a cancelled Updated Re-release of the game, featured an updated credits medley which included the standalone Sonic 3 tracks, alongside the Sonic & Knuckles tracks.
While it's exact purpose is unknown, many in the fandom speculate that it was originally planned to be a unique theme for Super Sonic ala Sonic 2, until it was replaced by the invincibility theme.
Besides the aforementioned tracks, there was another unused theme in the Prototype/ Sonic & Knuckles Collection that never got used at all.