Neither Roy nor Sheik appear as opponents or allies in Melee's Classic Mode (though Sheik can appear if Zelda transforms during battle). Ganondorf also cannot be fought, yet he can show up as an ally. Despite their absences, all three have their own intro poses programmed into the disc.

If Mr. Game & Watch absorbs 3 strong enough projectiles (Such as 3 fully charged PK Flashes) using oil panic and uses it against a shielding character, their shield will be broken, and Mr. Game & Watch will be sent flying back at extreme speeds. Unless there is a wall behind him to stop him, he will die almost instantly. This is known as the "Kamikaze Glitch".

Some of the trophies have strange reflection textures:

• The Ayumi Tachibana trophy has a reflection of a heavily embossed cat's face.
• Fire Kirby has a reflection of an inverted baby face.
• The Ocarina of Time trophy has a small reflection of the sky.
• Multiple trophies use a screenshot of Osohe Castle from the cancelled EarthBound 64.

Giga Bowser was a playable character at some point in development, albeit likely only for testing. He can be made into a playable character using cheat codes, and the announcer will even say "Giga Bowser" when he is selected. All boss characters are playable in some form using the debug mode.

DK's voice clip's were originally meant to be recycled from Donkey Kong 64, performed by Grant Kirkhope. But much like the original Super Smash Bros., it was decided giving DK a more realistic gorilla voice would better fit the game.

The music in Fountain Of Dreams is an orchestral remix of the Gourmet Race theme from Kirby Super Star. This remix was used in Kirby: Nightmare in Dream Land during the battle against King Dedede, and has since been recognized as the fountain's theme. Kirby: Nightmare in Dream Land was most likely in development during the creation of Super Smash Bros. Melee, and so the fountain's music was added as a teaser for the upcoming GBA game.

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.