The Rest Area Music in Allstar Mode is a remake of The Great Cave Offensive's Save Area Music from Kirby Super Star.

Allstar Mode itself may be based on Kirby Superstar's Arena Mode, as both have the player fighting a number of random enemies, finishing off with a consistent final opponent. Both modes feature a lobby between fights that displays which opponent the player will fight next, and a limited stock of healing items that do not replenish between fights.

The Ice Climbers' Target Test Room only has Popo (or Nana depending on the color) and instead of the Target Test music, it plays the Ice Climber music. This could reference the game Ice Climber, as Popo climbs to the top alone (unless there's two players), along with breakable blocks and scrolling clouds. The condor appears holding the last target which is referencing how an Ice Climber needs to grab onto the condor at the end of a bonus stage (which Target Test also is). The targets could also reference the vegetables in Ice Climber that the player needs to collect for points.

In the Stage Select screen, the symbol representing the stage of the game of origin appears briefly before an outline of the level is generated where the name of the stage is displayed. Although Final Destination has the traditional Smash symbol, being an original level, Battlefield strangely displays a shattered circle. The reason why is unknown.

The main menu theme sounds strikingly similar to the first part of the opening segment of the Super Nintendo RPG Terranigma, which was published by Nintendo in Europe. The composer for Melee may have taken inspiration from it.

Some of the characters' palette swaps reference past Nintendo character designs. For example, Kirby's white palette swap is a reference to his appearance in Kirby's Dream Land for the Game Boy.

Early trailers for Super Smash Bros. Melee show Samus' Grapple beam being more narrow and electric looking compared to the finished product.

When the game's language is set to Japanese in the international versions of the game, there are several differences in the trophy room's background. The NES changes to the Famicom, the Super Nintendo changes to the Super Famicom, the picture that reads "Super Smash Bros." is changed to say "Dairantou Smash Brothers." A Virtual Boy is also added.

The character select went through several changes. One design shows Kirby, Peach, Zelda, and the Ice Climbers missing from the character select screen.

The Yoshi's Story stage was originally different during the game's prerelease, featuring an extra plateau.

Since Star Fox Adventures was in development at the same time as Melee, the cast of that game would voice Fox (Steve Malpass), Falco (Ben Cullum), and Peppy and Slippy (Chris Seavor) within the English versions of the Corneria and Venom stages, despite both of them being based on Star Fox 64.

Ness' victory theme is an orchestrated segment of the Eight Melodies song from Earthbound.

The song "Mother", which plays in the stage Onett, is an orchestrated remix of four songs from the game Mother: "Bein' Friends", "Eight Melodies", "Mother Earth", and the jingle that plays before a battle begins.

Among the textures of the Mushroom Kingdom stage is a sushi board.

Event 22's name, Super Mario 128, is a reference to the series of experiments done to test technology that was eventually used in later games from Nintendo, as well as a reference to a sequel to Super Mario 64 that was never released.

There is an unused audio clip of Captain Falcon saying "Come on!" and "Blue Falcon". The Blue Falcon is Captain Falcon's final smash in Super Smash Bros. Brawl, and both voice clips appear in that game. It's possible the developers were experimenting with final smashes, just as they did in the original Super Smash Bros.

The bonus for getting a Star KO on all of the opposing team's members is called "Rocket KO". This may be a reference to Team Rocket from the Pokemon TV show, as they are commonly seen blasting off into the sky, punctuated by a star glint.

Like the original Ice Climber, Topis were changed from seals to a yetis due to the controversy of seal clubbing. Oddly enough, the English trophy description is exactly the same as in the Japanese.

When the game was revealed during E3 2001, the game's introduction sequence was played, followed by gameplay footage demonstrating each character's movesets. The only changes made when adding this into the game was to the gameplay footage.

In the PAL version of the game, the Rainbow Cruise stage is renamed to "Rainbow Ride", likely for consistency with the international versions of Super Mario 64.

A segment of the remixed DK Rap used in the Kongo Jungle stage has the Character Select theme from the original Super Smash Bros. mixed into it.