The character Wonder Cheerleader is modeled after Silvia from Viewtiful Joe. Her gun, Desperado, is also the name of a technique that Silvia learns in Viewtiful Joe 2.

Originally, the game was meant to have an all-star cast of Nintendo characters, plus characters from other games. Hideki Kamiya came up with the gameplay as a way to satisfy fans of all the different characters, as different gamers would prefer certain characters over others. As such, he decided to make all the characters appear at once, so that the fans could pick and chose which character to use. After the game was shelved for some time, it was decided to drop the all-star Nintendo cast to create an all new superhero cast.

Wonder-White's civilian name is Momoe Byakkoin. His surname Byakkoin ("百虎院") roughly translates to "White Tiger Temple", referring to the White Tiger of the West in Chinese astrology. Unusually, his first name Momoe ("百恵") is a feminine name and means "hundred blessings" in Japanese. White's first and last name each start with the same kanji "百" (hyaku), meaning "one hundred", referencing The Wonderful 100. The kanji is also seen on White's CENTINEL-Suit as a forehead emblem, and when it is damaged in later parts of the game's story (as seen in his Damaged Ver. 2 model), Spoiler:the emblem is damaged in such a way that makes it resemble the kanji "白" (shiro). Hyaku is derived from shiro, meaning "white".

Wonder-Magician's civilian name, Harry Silverfield, is loosely named after the illusionists Harry Houdini and David Copperfield. As a further connection to David Copperfield, the civilian name for Wonder-Rabbit (whose bio states that she works as Wonder-Magician's assistant) is Mina Kotkin, referencing Copperfield's real name David Seth Kotkin.

In Operation 002-C, if you fail Wonder Pink's quick-time event near the end of the mission, Wonder Pink will pull out her phone and start having a sped up conversation. Failing this event 10 times in a row will actually play the conversation in normal speed and reveal that she is talking to Wonder-Cheerleader.

Wonder Pink: Oh my god! What's happening girl?
Wonder-Cheerleader: Nothing, girl.
Wonder Pink: How's Joe?
Wonder-Cheerleader: He's good, but he stood me up last night! Said something about the last movie in a red hot trilogy!
Wonder Pink: He did what? Tell him to quit going to the movies all the time. Such a deadbeat!
Wonder-Cheerleader: I know.
Wonder Pink: No, I do not think he is red hot... You are a crazy girl.

This conversation heavily implies that beyond physical similarities, Wonder-Cheerleader is actually Silvia from another Hideki Kamiya directed series Viewtiful Joe (both characters are voiced by Christina Pucelli), and that “Silvianne Lumiere“ is just an alias. This is also referencing the unmade third game in the intended Viewtiful Joe trilogy.

In Operation 005-C, the boss battle is designed to play similarly to the Punch-Out series. The Gah-Goojin that the team pilots has two attacks, one obtained by collecting stars, the other by landing hits. These are references to the Star Punch in the NES Punch-Out!!, and the Knock-Out Punch in the SNES Super Punch-Out!!.

The character Wonder Wonderland is a clear reference to the book Alice's Adventures in Wonderland; her civilian first name is Allison, which is a nickname for Alice, while her banner is decorated with card suits and the quote "Down the Rabbit Hole".

Wonder Yellow's weapon, the Peta Peta Hammer, is modelled after the Japanese-toy called the Piko-Piko Hammer. "Piko-piko" is the onomatopoeia for the chirping sound that the toy-hammers make when struck down on something. "Peta-peta" itself is an onomatopoeia for "stick" as in gluing something, "stroke" as in painting something, and "pressing repeatedly", which is the most likely one for the weapon.

Jeanne, Bayonetta, and Rodin from the Bayonetta series make cameo appearances as unlockable characters, each having their signature weapons from the games. Unlocking them requires at least a Platinum-ranking on each stage.

The minor-character Wonder Rex is assigned to Great Falls, Montana in the USA. Montana houses the Museum of the Rockies, which holds the most dinosaur fossils in the United States, alongside other palaeontological finds. A great number of finds have been found in the state of Montana, most notably the largest Tyrannosaurus Rex skull discovered to date.

While her mother being a pro-wrestler explains Wonder Rex's Fist-based abilities and even costume, her father is titled as an archaeologist, which is actually a field of study specifically about human activity in the past. Palaeontology would be the correct field of study concerning dinosaur fossils.

During Wonder Pink's introduction scene, one of the poses she makes is the same pose made by the Title Character on the Japanese Cover of Bayonetta, another game developed by Platinum Games.

The minor character Wonder-Beetle has the title of "Not the Car, Not the Band", referencing both the Volkswagen Beetle car and the band The Beatles.

Wonder-Pink is originally from Romania and assigned in Transylvania, and uses a whip composed of "Belmont alloy", all of which are references to the whip-using Belmont family from the Castlevania series.

Wonder Yellow's civilian name (Ivan Istochnikov) comes from a Lost/Phantom Cosmonaut, which is a Soviet Cosmonaut that has entered space but has had their existence suppressed/wiped from history by their government. Ivan Istochnikov's story turned out to be a hoax, however.

The minor character Wonder-Gamer has a Famicom controller on top of his helmet. He is also assigned to Kyoto, the birthplace of Nintendo. This would be retained in the game's 2020 remaster, despite the removal of all Nintendo references and credits to accomodate the game now no longer being exclusive to Nintendo consoles.

Spoiler:Near the end of the game, when the Wonderful 100 unite into Ultra Platinum in the fight against Wonder-Jergingha, the Platinum Games symbol can be seen right before it becomes Platinum Robo.

The supporting robot character P-Star gets his name from the Platinum Games logo, which itself is the letter "P" next to a "star."

In the first meeting with Wonder Pink, Wonder Blue will comment "Hey, can we save the meet-and-greet for later!? We got a pain in the butt hedgehog to get rid off!", referencing the Gedie Dough-Goo they are under attack from and unable to defeat. The Gedie Dough-Goo itself is covered in blue spikes and has a spinning ball attack, making a strong reference to Sonic The Hedgehog.

This is also ironic, as Wonder Blue's english voice actor is Roger Craig Smith, who also voices Sonic the Hedgehog in the modern-gen Sonic games (Starting with Sonic Free Riders and Sonic Colors in November 2010).

In the news report shown during Bayonetta 2's opening cutscene, the mission complete music from Wonderful 101 can be heard in the background.

The enemy known as 'Gatcha' is modeled after Japanese capsule machines known as Gachapon. Like a Gachapon machine, the enemy features a knob that, when turned, causes it to dispense round capsules containing an object.