Episode 1.01: A janitor is briefly seen at the Superman Museum wearing a costume that resembles that of Booster Gold, and is preceded by the appearance of a robot that looks just like Booster's sidekick, Skeets. This is a reference to his job in the Metropolis Space Museum previous to becoming a hero in the 20th century. In addition, the inhabitants of New Metropolis resemble some of the alien species that make up the Green Lantern Corps, including the natives of Xudar and Barrio III.
Episode 1.02: An alien creature Superman and the Legion are fighting in space is noticeably similar to a Kryptonian creature that attacked Jor-El, Superman's father, in the pilot episode of Superman: The Animated Series, "The Last Son of Krypton".
Episode 1.03: In this episode, Alexis steals a bike belonging to a New Metropolis citizen who resembles Lobo. In addition, a satellite/space station resembling the Justice League Watchtower is seen and struck during a ball game. Alexis's story and character also seem a Legion-era analogue of Lex Luthor and most likely his descendant, respectively. In fact, her prison uniform clearly has her last name written on it in Interlac: "Luthor". Also "Lex" can be a diminutive for either Alexander or Alexis.
Episode 1.05: In the center of the main arena, there's a banner which reads, in Interlac: "Batman Lives".
Episode 1.06: Prisoners in the Phantom Zone resemble Superman's foes, Doomsday and the Pre-Crisis versions of General Zod and Faora. What's more, Drax's characterization is reminiscent of Zod himself, and numerous elements of his costume such as the big Z on his logo and origin hint that his origin is somehow connected to Zod. His two pets also heavily resemble an alien monster adopted by Bizarro in the Superman: The Animated Series episode, "Little Big Head Man". The Phantom Zone projector is also identical to the one used in Superman: The Animated Series and Justice League Unlimited.
Episode 1.07: Zyx is patterned after Superman villain Mr. Mxyzptlk, in both powers and demeanor (playful at first, but soon becomes malevolent). In addition, Zyx's first costume is based on Mxyzptlk's Silver Age costume. Zyx's helmet also resembles the Justice League of America villain Brain Storm. In another scene, when Zyx is creating various objects, he briefly conjures the Emerald Eye, a Green Lantern power battery, and Doctor Fate's helmet. Later, when fighting Superman, he briefly turns into a creature resembling Starro.
Episodes 1.08 and 1.10: Prospective applicants for the Legion who did not eventually form the series' version of the Legion of Substitute Heroes in episode 1.10 included not only some who did join the comics version (Antennae Lad, Double Header, Polar Boy, Fire Lad, and Night Girl), but also other rejects (such as Quake Kid, Polecat and The Mess), and even a Legionnaire (Invisible Kid).
Episode 1.09: The Mining robots which Superman and Timber Wolf battled toward the end have a very similar design to the space exploration robots built by the Waynetech/Luthorcorp partnership in the episode of Superman: The Animated Series episode "World's Finest". Brainiac 5 also rattles off the names of the colors after saying "green rocks kill the last son" he then lists them as coming in Blue, Red and Gold, all of which were variations of Kryptonite. In addition, Brainy inadvertently reveals that Superman is affected by the red sun while they are on Zuum, though it is ignored, as he said "Superman shouldn't play with red ants."
Episode 1.10: One of the colorizations Color Kid gives Superman matches the DC Animated Universe animated version of Bizarro. Other colors include red (resembling pre-Crisis Superman Red), blue (resembling pre-Crisis Superman Blue), and green (giving a sense of Kryptonite poisoning). The beginning of the episode shows a plant monster that attacks the Legionnaires, similar to one that appears with Poison Ivy in Batman: The Animated Series.
Episode 1.12: Brainiac 5 mentions a "Great Crisis", a reference to Crisis on Infinite Earths and/or Final Crisis. The Sun-Eater also appears in this episode, this is the third time the Sun-Eater has been included in a Legion storyline.
Episode 1.13: Ferro Lad's sacrifice echoes his comic book counterpart's own fate against the Sun-Eater.
Episode 2.02: The now adult and seasoned Superman tells his clone that he reminds him of a friend of his that was a grim loner that ended up becoming a valuable member of a team. Such a description fits Superman's Justice League teammate, Batman. He also mentions Wally (the third Flash).
Episode 2.08: A Superman android appears in the Fortress of Solitude, visually resembling the Superman villain Cyborg Superman. A dog and cat resembling super-pets Krypto and Streaky are also seen in Kandor. Brainiac's skull ship also appears in this episode.
Episode 2.09: The younger Legionnaires seen in the episode's flashbacks are depicted wearing their Silver Age costumes.
Episode 2.12: Some characteristics of Brainiac 5's evil form were previously linked to Brainiac 13 (such as having tentacles coming out of his back). Brainiac 5 also remakes Imperiex's ship into his own version of the Brainiac skull ship. Many Legionnaires from across the various version of the comic book Legion are also seen as background characters in this episode, but play no role beyond this.
Episode 2.13: The scene where Brainiac 5 holds Superman is the same as the introduction scene for this season of Superman holding Brainiac 5. Also, the scene inside Brainiac 5's head where several other Brainiac 5's appeared also mimics a scene in Reboot Legion where several Brainiac 5's tackle a telepath who invaded Brainiac 5's mind. In the show, the clones tell Brainiac 1.0 to get out of his head; in the books they told the telepath her choices were to leave the information she found in his head behind or not leave at all.