- "Perchance to Dream" consists mostly of an extended dream sequence created by the Mad Hatter to keep Batman trapped in a dream world. After Batman finally wakes up into reality, he looks at the elaborate head rig created by the Mad Hatter, and calls it "the stuff that dreams are made of".
- In "Off Balance", Batman asks Talia whose side she is on. "That would be telling" she replies. Almost every episode of The Prisoner (1967) started with that dialogue.
- In "Nothing to Fear" the security guard in the beginning is reading a comic book called Tiny Toon Adventures.
- Star Labs is also cited in a list of potential sources of the Scarecrow's fear gas.
- In a later episode, "Torch Song", Bruce is discussing a ongoing case with Barbara Gordon. When he asks, "What are you doing tonight?" she replies, "The same thing we do every night, Pinky." He does not get the reference.
- At the start of "Joker's Wild", the Joker is whistling the Looney Tunes theme.
- Not two minutes later, he busts out a Beaky Buzzard impression.
- In "Christmas with the Joker", he sings "Jingle Bells, Batman Smells" as he escapes Arkham.
- In "You Scratch My Back", a list of ships includes Andrea Doria, SS Minnow, HMS Bounty, and Poseidon.
- Two-Face's suit is a rather obvious reference to the famous Scarface (1983) poster.
- In "Two-Face: Part 2", while robbing one of Rupert Thorn's fronts, Two-Face says "Do not attempt to adjust the picture, I'm in control!"
- In "The Laughing Fish" Joker pulls a wrench out of a box with the words "Binford Tools" written on it.
- In "The Mechanic", one of the Penguin's henchmen celebrates their apparent victory against Batman by saying "T-t-t-that's all, folks!"
- In "Beware the Creeper", not only does the Creeper look similar to and act just like Freakazoid!, but he talks to a woman through her window and when she screams and runs...The Creeper: Okay, I love you, buh-bye!
- The robots in the opening to "Deep Freeze" are based on both Castle in the Sky and The Mechanical Monsters.
- Cybertron Industries appears in "Heart of Steel".
- Karl Rossum, the owner of Cybertron Industries and one of the pioneers in A.I. research and robotics, is named for Capek's play R.U.R. (for Rossum's Universal Robots), the origin of the term "robot."
- In addition, Karl Rossum is voiced by William Sanderson in a clear nod to his role on Blade Runner, with HARDAC's robot replacements being very similar to Replicants.
- Poison Ivy's license plate in "Harley and Ivy" is "Rosebud".
- And a few seconds after that Ivy tells Harley, "This could be the beginning of a beautiful friendship."
- "Robin's Reckoning: Part 2" has a shout out to AKIRA when Dick strikes a similar pose to Kaneda on his bike.
- At the end of "Joker’s Wild", the inmates in Arkham are watching Bugs Bunny cartoons.
- To It's the Great Pumpkin, Charlie Brown, where one thing Sally said to Linus in the pumpkin patch was, "If you try to hold my hand, I'll slug you!"; near the beginning of "Joker's Wild", in the lounge at Arkham Asylum, Joker cozies up next to Poison Ivy, and teasingly says, "If you hold my hand, I'll slug you!"
- The poster for the magician The Great Prosciutto in "Be a Clown" is a cartoonified portrait of Alan Moore.
- Anthony Romulus from “Moon of the Wolf“ has eyebrows that meet in the middle which, according to The Company of Wolves, is a sign that a person may well be a werewolf.
- "Trial" has Batman capturing the skull gang's leader, who wears a T-shirt that's exactly like The Punisher's logo.
- At one point when Batman and Robin are artificially sped up, Robin quips: "Faster than a speeding bullet..!"
- Adam West, Batman of Batman (1966), guest-starred in "Beware the Gray Ghost".
- "Harley's Holiday", Harley Quinn, upon returning to Arkham, says the line, "Home again, home again, jiggity jig." It's a reference to the scene where one of the toys says the same line when J.F. Sebastian comes home with a woman in Blade Runner.
- In "The Clock King", the streets have the names from various comics and animation artist who worked at Batman: Keith Weesner, Jack Schiff, Jerry Robinson, Norm Breygfole, Alex Toth, and Kurt Busiek.
- "Catwalk" has Selina Kyle quoting Rudyard Kipling's "The Cat who Walked by Himself."
- The title card◊ for "Riddler's Reform" bears a resemblance to a famous page in The Amazing Spider-Man (1963) #50.
- In "Joker's Wild", Batman exclaims "Camelot" when he encounters the model detailing the original theme of Kaiser's casino.
- In "Harlequinade", when Harley does her impromptu musical number she instructs the orchestra that she will be singing in the key of A flat, as Lina does for her impromptu musical number at the end of Singin' in the Rain (and in very nearly the same nasal voice).
- In "Christmas with the Joker", the taxidermy horse that "pulls" the Joker's sleigh in his pirate TV broadcast has a single trimmed tree branch tied to its forehead with string to pass it off as a "reindeer". Joker also knocks over a pathetic-looking bare-branched little Christmas tree.
- In "Day of the Samurai", the antagonist's hideout is at 563 Tezuka.
- In "The Man Who Killed Batman", the Joker's eulogy for the presumed dead Batman starts thusly:Joker: Dear friends... Today is the day that the Clown cried.
- In "If You're So Smart, Why Aren't You Rich?" Batman immediately deduces the Riddler's reference to a lyric from the Oklahoma! song "Oh, What a Beautiful Mornin'." Robin fails to get the reference to "corn as high as an elephant's eye," and Batman has to explain it to him.
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