There are numerous references throughout Superman: The Animated Series to past incarnations of the Superman mythos, including the comics themselves and other media adaptations.
- In "Stolen Memories", Superman overcomes a laser fired by Brainiac by punching at it, which is the same as how he overcame a laser in the first Fleischer Superman Cartoon.
- Superman at first mispronounces the name Mxyzptlk as "Mix-ill-plick"... exactly the way it was pronounced on Superfriends.
- The show refers to Mxyzptlk as the source of legends about genies, imps and leprechauns, just like Lois & Clark. It also shares more-or-less the same dialogue about his weakness, though a different character responds here:Clark: "I can barely say your name forward." / "I can't even say your name forward, how am I supposed to say it backward!"Lois: "Well, you don't have to say it backwards, you have to get him to say it." / Mxyzptlk: "No, dope! You don't have to say it backward, you have to get me to say it!"
- In "The Last Son of Krypton: Part 1", one of the guards says "Great Rao!", which Superman often says in the Silver Age comics.
- In "Last Son of Krypton, Part 3", Lois tells Bibbo to have Clark call "Commissioner Henderson" if she is not heard from soon. Inspector William Henderson was a character originally introduced in the 1940's radio series as Superman's contact on the police force; he was later adapted into the television series and, eventually, the comics. His role was eventually supplanted by Daniel Turpin and Maggie Sawyer, two characters who would become important recurring characters within this series, and he is currently Metropolis's Police Commissioner. He is given a small role in “Feeding Time” and appears in the background in “Apokolips... Now!”.
- In "New Kids in Town" , Brainiac has one to Superman II:
- "At last, the son of Jor-El kneels before me."
- In "Target", when Lois Lane is trapped in the elevator Superman rescues her and says that "I believe this is your floor," the same line he spoke to Lois when rescuing her from an elevator in Superman II.
- The comet that Darkseid will use to destroy the Earth in "Little Girl Lost" is Fleischer's Comet.
- The Mxyzptlk comic strip in "Mxyzpixilated" (See Freeze-Frame Bonus above) is written by Siegel and Shuster, the original creators of Superman. Both the episode and the comic feature Mxy looking for "McGurk," a hulking strongman/Expy for Auguste Rodin's " The Thinker," that Mxy searched for in his very first comic book appearance.
- He also turns Jimmy Olsen into a turtle, a reference to his "Turtle Boy" persona, one of the most memorable of his many guises.
- Bizarro gets a hideous alien "dog" which he calls "Krypto".
- Krypto himself has a cameo in the pilot, and Streaky the cat lives on the Kent's farm. At one point, Mxyzptlk makes the latter fly - a reference to its Silver Age superpowers.
- The episode where Bizarro tries to "rebuild" Krypton is called "Bizarro's World."
- At Mr. Mxyzptlk's trial, his wife appears to offer up evidence that his obsession with Superman means he is not responsible for his actions. One of the pieces of evidence she puts forth is a copy of Action Comics.
- During Maxima's tenure with the Justice League of America, it was revealed that her heavy-handed and reckless methods of ruling Almarec caused a lot of resentment among her subjects, to the point that when the elders banished her, there was a great deal of popular support for said banishment. In this series, as soon as she leaves the planet to court Superman, her handmaiden organizes a coup to save her people from her rule.
- "Monkey Fun" was apparently a remake/homage to a similar episode of the 60s Superman cartoon.
- The toy monkey is named Beppo, which is the name of the Super Monkey.
- In "The Main Man," one of the creatures in the Preserver's collection is Starro the Conqueror, a recurrent Justice League of America villain. Superman saves it, along with the rest, and puts it in his Fortress' alien zoo, which will come back to bite him in a big way later on.
- In "In Brightest Day...", the Air Force jet that Sinestro slams Kyle Rayner into belongs to "Col. Hal Jordan."
- In ""Tools of the Trade"", Superman catches a car falling off the cliff. His pose as he holds it is very similar to the cover of Action Comics 1, Superman's first appearance.
- "Mxyzpixilated" is extra-extraordinarily meta: Mr. Mxyzptlk is introduced wandering into traffic looking for a man named McGurk, as he was in his first appearance. Superman mispronounces Mr. Mxyzptlk's name exactly the way that the Super Friends production team decided to pronounce it. Mr. Mxyzptlk himself all but crosses the Fourth Wall, turning Lois into a horse
and Jimmy a turtle, making the Kents' cat flight-capable, and starring in his own private newspaper comic strip by "Siegel and Shuster," the creators of Superman. - "Little Big Head Man" shows Bizarro's created a model of a square planet, namely Htrae, Bizarro Earth from The Silver Age of Comic Books. Then Mr. Mxyzptlk's girlfriend Ms. Gsptlsnz summons up a real-life Action Comics issue advertising Mr. Mxyzptlk on the cover.
- "The Last Son of Krypton": When Martha Kent finds the infant Kal-El, she considers the names Christopher and Kirk, in reference to Christopher Reeve and Kirk Alyn, who also played Superman, before deciding on Clark.
- "My Girl": Superman uses his cape to shield himself and Lana against molten lead, evoking the Superman Theatrical Cartoon The Mechanical Monsters.
- At one point in "Apokolips... Now!", Superman can be seen fighting Parademons in front of a building that resembles the Hall of Justice, likely a subtle reference to Darkseid and his forces making their first animated appearance in the final two seasons of Super Friends.
- "Knight Time": When Superman (as Batman) lifts the statue, Robin "explains" it by saying that he has been "working out". Clark Kent does the same thing in Superman II.
