Kirby
Yellow: A reference to the early plan to make Kirby yellow, as well as the second player's character from Kirby's Dream Course.
Light Blue: Looks like the Ice Kirby power-up.
Red: Echoes his coloring as Fire Kirby.
Green: His coloring after gaining the Plasma power-up in Kirby Super Star.
Grey: Recreates his appearance in Kirby's many Game Boy games.
Orange: --
Purple: Is this what Meta Knight looks like without his mask?
Link
Red: The Goron Tunic Link wears to survive in lava-filled temples.
Blue: Link can breathe underwater when wearing this Zora Tunic.
Purple: One of the alt colors from the Four Swords spin-offs.
Yellow: --
Black: Clearly he's been replaced by Dark Link, his evil twin.
White: The tunic Link wears at the start of Skyward Sword.
Black/Yellow: Link's Fierce Deity transformation from Majora's Mask.
Little Mac
Yellow Gloves: Mac's outfit during Punch-Out!!'s Title Defense Mode.
White: Possibly referencing a coloring glitch for when Little Mac wins in NES Punch-Out!!
Blue/Red Gloves: His outfit during the World Circuit Challenges.
Blue: --
Orange: --
Blonde: Mac is looking fierce in this tribute to the Super Punch-Out!! protagonist's hair style.
Pink Sweatsuit: Mac's clothing during the iconic training sequence in the NES version.
Little Mac (Wireframe)
Green Trunks: All the wireframe looks reflect Mac's appearance in the original arcade release of Punch-Out!!
Red and White Trunks: --
Black Trunks: --
Blue and White Trunks: A wireframe version of his World Circuit look.
Blue Trunks and Gloves: --
Yellow: --
Blonde Hair: A reference to Super Punch-Out!!'s wireframe look.
Green: The reverse of his classic workout gear.
Lucario
Purple: --
White: --
Grey: --
Teal: Perhaps a reference to his pre-evolved form, Riolu.
Blue: --
Green: --
Pink: --
Luigi
Orange/Blue: An imitation of Mario's color scheme in Pinball for NES.
Pink: Luigi's outfit from the first Wrecking Crew games.
Light Blue: --
Green/White: A recreation of the powered-up Fire Luigi.
Purple: Obviously a tribute to his evil clone, Waluigi.
Yellow/Blue: Perhaps a reference to his appearance in the original Mario Bros. for arcade?
Orange/Blue: --
Mario
White/Red: The iconic Fire Mario look.
Light Blue/Pink: A recreation of Mario's look on the cabinet art for the arcade version of Mario Bros.
Purple/Yellow: Mario is poaching the style of his clone, Wario.
Grey/White: This is the outfit he wore in the Japan-only Wrecking Crew '98.
Green: Looks like Luigi, specifically his appearance in the first Mario Bros. title.
Red, White and Blue: This patriotic design is what he wore in NES Open Tournament Golf.
Purple: After doing Wario, why not make the set complete by copying Waluigi?
Marth
Red: Fire Emblem's standard enemy coloring.
Green: Fire Emblem's coloring for ally characters.
Black/Yellow: --
White: References Leif, the star of a Japan-only Fire Emblem release.
Blue and White: This is the look of Eliwood, another Fire Emblem character not known outside of Japan.
Yellow: The partner color from Fire Emblem franchise.
Blue/Purple: A tribute to Roy, his fallen comrade.
Mega Man
Red/White: Each of Mega Man's alts is based on a different power-up from his many games. This is the combo he wears when summoning his robo-dog, Rush.
Green/White: This is for the Leaf Shield.
Orange/Yellow: The Metal Blade outfit.
Blue/White: This could apply to the Water Shield, Ice Slasher, and many other special abilities.
Green/Yellow: This one applies to the Slash Claw.
Red/Yellow: These outfits are for assorted power-ups, like the Flame Sword and the Magma Bazooka.
Black/Yellow: And lastly, this color combo is used for the Thunder Beam.
Meta Knight
White: Looks like Kirby's Paladin, the holy knight of the franchise.
Red: --
Green: --
Black: A tribute to Meta Knight's earliest appearance in the concept art for Kirby's Adventure.
Pink: This is a cute joke to make it look like Kirby is dressed like Meta Knight.
Purple: It imitates the appearance of the Galacta Knight from Kirby Super Star Ultra.
Black/Grey: This one is meant to look like Dark Meta Knight from Kirby and the Amazing Mirror.