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"Deep Cover For Batman!"/"Game Over For Owlman!" has references to Earth-3's Owlman (evil owl-themed mirror-universe Batman), the ElseworldsLeatherwing (pirate Batman) and Red Rain (vampire Batman), and the once-canon "The Batman Creature" (hulking creature Batman).
"I'm Batman...". Also, in "Game Over For Owlman!," he calls the Batmobile by remote, and stops it via voice command, exactly like how he does in the 1989 film.
Batman's spare Batmobile in "Game Over for Owlman!" is the version used in the comics from 1941 to 1950. (His main one looks more similar to the version in the '60s TV show.)
The impostor Batman looks a lot more like DCAU Batman than this version does, because it resembles the old Bob Kane Batman (right down to the purple gloves); there's even a Homage Shot of his first pose in costume from the original origin story, which itself was a Homage to a pose from Tarzan. Owlman's own costume also has more elements of this look than any of his comics counterparts, particularly the outward pointing ears; this also makes him look quite similar to Justice Lords Batman from Justice League.
And in a later episode, a flashback features the real Batman as a rookie hero earning his keep with the Justice Society and wearing nearly the costume as Owlman-as-Batman
Speaking of which, the people of Rann dress a lot like DCAU Kryptonians - two of the first ones we see even resemble Jor-El and Lara.
The title of "Mystery In Space!" (as well as the setting and the guest stars) is taken from the name of a 50s-60s comic, though it was dusted off for a miniseries as recently as 2006.
Batman's torn costume in "Trials of the Demon!" gets repaired into his Gotham by Gaslight garb.
In the "Trials of the Demon!" cold open, Scarecrow has four Mooks dressed up in themed outfits to surround and attack Batman one by one, exactly like how Adam West used to fight every week.
In "Menace of the Conqueror Caveman!", Booster Gold mentions that Skeets can turn into a giant insect, a reference to the plot of 52.
Robin's costume in "The Color of Revenge!" is a dead-ringer for the original Earth-2 version of Robin, who kept his Robin identity through adulthood and modified the costume accordingly.
Also, the episode starts off with the two of them getting a call from the Commissioner, sliding down fireman poles into the Batcave, and leaping into the Batmobile, just like the Adam West version.
Not to mention the Shakespeare bust hiding the button to the secret entrance, music based on Neal Hefti's score for the 1966 show, a quick cut of them putting their seatbelts on in the Batmobile (which looks more like the George Barris version), a wall-climbing moment, Dutch Angles, and a "Holy ____!" Catch Phrase! The only thing we didn't get were superposed sound effects (but see "Legends of the Dark Mite!")...
In "Legends of the Dark Mite!", when Bat-Mite fantasizes that he is Batman, he stands on a rooftop dramatically while lightning strikes in the background, just like in the opening to Batman: The Animated Series.
Bat-Mite's fantasy also has a clear visual reference to Detective Comics #365, "The House the Joker Built", with a funhouse having a Joker-shaped door.
The fantasy sequence also references Detective Comics #140, the debut of the Riddler (Bat-Mite trapped in the bent-wire cage) and overall parodies the Bob Clampett cartoon "The Great Piggy Bank Robbery".
All of the villains summoned up in Bat-Mite's fantasy (Mr. Polka Dot, Tiger Shark, Mr. Zero, Rainbow Creature et al) were actual villains who had appeared in Silver AgeBatman comics and, in a handful of cases, virtually never since.
The title of "Legends of the Dark Mite!" is a play on that of the classic BTAS episode "Legends of the Dark Knight" — and the anthology comic that inspired it.
Lashina's joining forces with Jonah Hex in the coda of Duel of the Double Crossers is possibly a reference to her being one of the very few Female Furies to have served a stint on the side of the good guys in the comics. (Not that it ended well for her print counterpart.)
The final number of "Mayhem of the Music Meister!" sets up Black Canary and Green Arrow as a couple.
In "Aquaman's Outrageous Adventure!", every time AQUAMAN sees another hero and decides to head out to help, there's a brief flash to a Superfriends-style title card, complete with the classic scene transition noise from Superfriends. You know the one.
Arthur Jr., introduced in this episode, wears the deep sea camouflage costume briefly worn by AQUAMAN in late 80s comics.
Also, the US map AQUAMAN's family uses for their vacation contains pretty much every superhero home city (Smallville, Blue Valley, Coast City, Star City, Fawcett City, Middleton, Dakota, and Metropolis).
In "Sidekicks Assemble!" a meeting between the heroes and their sidekicks takes place at the Hall of Justice from Superfriends. Also at the end, Nightwing makes his debut in his original "disco" costume.
The entire episode is also one extended reference to the Silver Age Teen Titans, while Dick becoming Nightwing at the end is a nod to the 80's New Teen Titans run (where he first took up the Nightwing identity).
The Metal Men being introduced during a fight with Chemo is a nod to Chemo first appearing in the comics as an enemy of the Metal Men.
The Gas Gang are provided the early 90s version of the Metal Men's backstory — they were human assistants and friends of Doc Magnus before being transformed by an accident.
The Gibble People from "Rise of the Blue Beetle" have the exact same texture as the shapeshifting alien race from the Justice League pilot arc.
In the opening for "Chill of the Night!" Abra Kadabra turns a crowd into an army of puppets just as he once did to The Flash.
Adam West voices Thomas Wayne in "Chill of the Night!" and has this exchange with Batman:
Batman: How's your aim? Thomas Wayne:Impeccable, old chum.
Joker owing his thanks to Joe Chill for creating Batman may be a sly nod to the 1989 Batman movie where it was the Joker himself (long before his fateful accident) who killed Bruce's parents.
"Siege of Starro" includes a Homage Shot of the titular villain's first appearance on the cover of The Brave and the Bold #28, though the heroes involved are different.
One of the Faceless Hunter's trophies is Gleek the Space Monkey from Superfriends. He has others of a Justice League Thanagarian, the Silver Age Brainiac (A Coluan?) and a Parademon.
The Metal Men combining to form Alloy is a reference to Alloy from Kingdom Come, who is described, you got it, as the combined form of the Metal Men.
It may double as a reference to a couple of Silver Age Metal Men stories in which the whole team is alloyed together into one huge robot, though they couldn't combine or separate at will in those.
Blue Bowman is one of the original evil mirror versions of the heroes, but his name isn't. Z list Batman villain Signalman used it for a short time in the 70s.
Mr. Zero, Katana and Black Lightning start off in different outfits, but gain costumes reminiscent of their comic counterparts in "Chill of the Night!" & "Siege of Starro!" part one.
The teaser for "The Last Patrol" has two. First, Batgirl is introduced fighting Killer Moth, the first villain she fought in the comics. Secondly, a large overgrown caterpillar can be seen which resembles Silkie from the Teen Titans cartoon (originally created by Killer Moth.)
Also, it's part of a flashback seen while in a Death Trap by the Penguin. It's a stretch, but the choice of Penguin for the villain in the here-and-now after a Killer Moth flashback makes sense: in The Batman, Killer Moth worked for the Penguin (and in that story, he was mutated from a human form similar to his TB&TB look to his monstrous current form.)
Though the differences between the DC Universe and the Brave and the Bold at the time TB&TB was made (Barbara Gordon still being Batgirl rather than Oracle and Huntress wearing her Silver Age costume are the two biggest examples) made an accurate adaptation impossible, the Birds of Prey homage episode is written in the style of the comic (unsurprising, seeing how they had the same writer), and even features the heroines calling themselves "The Birds of Prey" during a musical number.
Part one of "The Siege of Starro!" has a scene where Captain Marvel fights a mind-controlled Guy Gardner. In the comics, the two did not like each other during their time with the Justice League, where Guy routinely referred to Marvel as "Captain Whitebread".
In the "Mask of Matches Malone!", Two-Face rescues the Birds of Prey dressed as Batman. While not exactly the same costume, Two-Face has donned a cape and cowl before, as part of the Battle For The Cowl storyline. (Technically afterwards, but still.)
The sideshow in "The Last Patrol!" features a variety of posters for Doom Patrol related acts: Rhea Jones, a surreal magnetic butterfly woman from Grant Morrison's run; Baboshka, a human stacking doll also from Morrison's run; Beast Boy (Yes, that one) shown in his original pompadoured glory; Shasta the Living Mountain from Morrison's satirical Doom Force issue; Flex Mentallo, a Charles Atlas inspired superhero that got DC in all sorts of trouble; and Dorothy Spinner, a monkey faced girl that can bend reality. Notably, Flex Mentallo's name isn't on his card. Gee, I wonder why.
And for that matter, Zahl's Parisian plot hinges upon a barely seen painting- a nod to the Painting that Ate Paris from Morrison's run. When the Patrol breaks up, Negative Man can be seen in the long coat and glasses from Morrison's run. And lastly, the ending of the story is based explicitly on the Doom Patrol's final Silver Age story from Doom Patrol #121, in which the Doom Patrol sacrifice themselves to save fourteen fishermen in the Maine town of Codsville.
The Asian woman and African-American man who lead the chant of "We're all the Doom Patrol" might be Celsius and Tempest of the Paul Kuppenburg run.
After arriving in a blasted present, Booster Gold exclaims "oh, boy." This is a reference to his second series, the use of which was in turn a reference to Quantum Leap. Double ref!
The episode "Emperor Joker" has buttloads. To start things off, the opening has references to Detective Comics #241 "The Rainbow Batman!", Batman #134 with the Rainbow Creature (who appeared earlier in "Legends of the Dark Mite!"), and Firefly's original shtick with colors and light instead of fire. The episode proper has Bat-Mite reading an entry out of Who's Who.
Bat-Mite's Joker museum from "Emperor Joker" features:
The covers to Batman #251's "The Joker's Five-Way Revenge" (notable for reintroducing the Joker as a homicidal madman), The Brave and the Bold #191's "Only Angels Have Wings", and Batman #11.
Sculptures depicting "The Joker's Utility Belt" from Batman #73, "The Laughing Fish" from Detective Comics #475 (the fish themselves appear multiple times throughout the episode), and the iconic Jim Aparo Pietà Plagiarism image from "A Death in the Family" (Batman #426-429) showing Batman cradling Jason Todd's dead body - complete with a completely out of place explanation for how the fans killed off Jason in a vote off(!)
Replicas of the Jokermobile and Jokergyro, introduced in Batman #37 and used in multiple Silver Age stories and the 2000s Grant Morrison run on Batman.
Later in the episode, Bat-Mite gets stuck in a jester's outfit identical to Harley Quinn's most famous costume- while Harley stays in her Mabel Normand outfit.
Joker-Mite also looks a lot like Jack Nicholson from the 1989 Batman film.
Also, the battle between Superman and Batman is almost identical in shots for the battle between Superman and Darkseid in the final episode of Justice League Unlimited. Presumably to show how Superman isn't holding back in this fight.
The episode is also filled with dozens of references to Silver Age "Superdickery" Superman stories. Jimmy Olsen even lampshades it. Mayor Swan is named after artist Curt Swan, who drew many such stories.
Superman turning into a jerk by red kryptonite is also a nod to Smallville, in which red kryptonite removes Clark's inhibitions and makes him act on erotic and selfish emotions.
All three of the "Batman's Greatest Cases" cold opens are mashups of memetastic Silver Age stories and other Silver Age hoopla. The first mixes the Rainbow Batman from Detective Comics 241 with the original Firefly from Detective Comics #184 and the Rainbow Creature from Detective Comics 134; the second mixes the Mummy Batman and Robin from Detective Comics 320 with King Tut (AKA the Pharaoh) from the Adam West show, complete with buttermilk; the last mixes the Jungle Batman from Batman 72 with Golden Age Catwoman and Mogo the Bat-Ape from Batman 114.
The costume Catwoman wears in this episode is one of her comic counterpart's older Silver Age looks.
The end of "The Knights of Tomorrow!" shows the new Batman and Robin punching Mister Toad, Professor Pyg, Eduardo Flamingo and other villains introduced in the "Batman and Robin" comic.
Also, when lampshading his Joker immunity in the same episode, Joker notes that he's been "blown up, knocked down smokestacks and fed to sharks," three ways he seemed to die in famous storylines (the last two happening in "Mad Love" and "The Laughing Fish" respectively, two stories famously adapted in this show's predecessor BTAS).
The only known story where the Joker blew up is alongside Red Skull in the Elseworlds Batman/Captain America.
Actually, the Joker was thought to have died at the end of "The World's Finest" when he was still in an aircraft as it blew up.
Earlier in the episode, an aged Bruce Wayne was seen to sport a mustache much as he did at the beginning of DKR.
The Joker's son has a prominent widow's peak (a classic sign of male pattern baldness), a heftier build than his old man, and at one point in the episode wrecks a museum — all of which point to being at least partially inspired by Jack Nicholson's Joker.
The Batman Museum features a "Hall of Holy-isms", referring to Burt Ward-as-Robin's "Holy X, Batman!" catchphrase from the 60's Batman TV show. There's also a statue of Poison Ivy that looks almost identical to her The New Batman Adventures-era BTAS character model.
The concept of a Batman Museum in general may be a reference to the Flash Museum.
The Wonder Woman opening of "Scorn of the Star Sapphire" had the old live action Wonder Woman theme song playing in the background. And when she throws her tiara they use the live-action show's sound effect.
The premise of Triumvirate of Terror! seems to be based on a similar Silver Age story where two foes of Green Arrow and Aquaman traded nemeses.
Superman, Wonder Woman, and Batman meeting in a diner recalls Kingdom Come — but not as much as the future seen at the end, where the three of them look exactly like they do in Kingdom Come.
The President seen in the future is Prez Rickard, the 18 year old POTUS and star of his own self-titled series in the early 1970s.
The Creature Commandos section of "Four Star Spectacular!" is an adaptation of a Commandos story from Weird War Tales #100, with Dr. Myrra Rhodes (who wasn't with the team yet in the original story), the Ultra Humanite, and, of course, Batman added in. The Humanite's dinosaur body may count as a gag in and of itself- it's only been used once, in All-Star Squadron, and was never seen on Dinosaur Island, where it was said to be taken from.
In "Shadow of the Bat!", Vampire Batman asked if Martian Manhunter's blood is green (which Two-Face asked Riddler in Batman Forever). At one point, he turns into a demonic bat-creature like in Scarecrow's hallucination in Batman: The Animated Series episode "Nothing to Fear".
There are two for Teen Titans in the "Worlds War" short. First is the Alien that the Titans fought in "Stranded" in one of the worlds that Adam Strange planet-hopped to. And the next is a short appearance of Le Blanc falling on the ground after a fight with Batman. You don't see his face but his clothes look like they do in the show.
In "Mitefall", Bat-Mite has Batman use handguns, like in the Golden Age and Batman: Year Two.
The episode's title is a reference to the infamous Knightfall storyline.
Actually, there was a book named Mitefall, which was a Knightfall parody and where the episode's title comes from.
In the same episode, the alternate outfits Batman wore throughout the episode were based on various Batman toys released in the past.
Also, Batman has a daughter, a la the Golden Age/Earth-Two Huntress who's the daughter of Batman and Catwoman.
Having Bat-Mite be part of the final episode (and the final issue of the comic book adaptation) is a reference to his appearance in the final issue of the comic book series that inspired the show.
Ambush Bug and Batmite popping out of the windows in the building Batman climbs in is a reference to the 'Batman Window cameos' used in the 60's camp show.
The final group shot in the series finale, which shows Batman and his heroic allies saying goodbye to the viewers, has the number of the stage in the back lot saying ‘Stage 27’, referring to the 27th issue of Detective Comics, Batman's debut. ◊
After being shocked by Black Lightning, Wildcat says: "It's gonna take a whole lot more than a little Static Shock to slow this old man down".
The "Crisis: 22,300 Miles Above Earth!" cold open featured Mr. Freeze with a Germanic accent making awful puns, a reference to Arnold Schwarzenegger's infamous portrayal of the character in Batman & Robin.
The African member of the Batmen of All Nations is Impala, who isn't actually based on Batman but was a member of a similar Multinational Team in the comics, the Global Guardians.
In "The Super Batman from Planet X!", the Batman of Zur-En-Arrh resembles the DCAU Batman. His secret identity Tlano even looks identical to Bruce Wayne as he looks in the earlier seasons of Batman: The Animated Series.
In a rather obscure example, Batman of Zur-En-Arrh's robot butler is named "Alpha-Red". This is a nod to an anime-inspired Batman show Bruce Timm had pitched after Batman Beyond, which would've been set in the future and featured a trio of teens as the new Batman, Robin, and Batgirl. Not much is known about the series, but Timm has stated the kids would've used a butler A.I. named Alpha-Red.
In "Bold Beginnings," Green Arrow comments that as evil as the Cavalier is, he likes his goatee. In practically every other modern incarnation, Green Arrow has one himself. The same episode mentions Batman having gone through a "dark loner phase" before the events of this series.
In the episode "Powerless!", during "Aquaman's Rousing Song Of Heroism", Aquaman takes on the appearance and powers of other heroes. His appearance as Martian Manhunter shapeshifting into a snake is an exact copy of J'onn's power-display in the Justice League title sequence.
The training outfit that Captain Atom wears after losing his powers in "Powerless!" is his original costume from his first appearance in Charlton Comics.
Beneath his mask, Clock King is drawn to resemble Walter Slezak, who played the character in the 1960s Batman live-action series.
An episode about a mixer between the JSA and the JLI is named "Crisis 22,300 Miles Above Earth!", imitating the Idiosyncratic Episode Naming for the Silver Age JSA/JLA crossovers.
In fact the title is an explicit Shout-Out to "Crisis Above Earth-One!", the story that killed off the Golden Age Mr. Terrific (and took place at a mixer between the JLA and JSA).
Shirley Walker's Batman leitmotif from the DCAU appears in the 'Mazing Man sequence of "Four Star Spectacular!".
The first episode begins with Batman fighting Clock King with help from Green Arrow, referencing how the Clock King was originally a Green Arrow villain.
In "The Power of Shazam!", Dr. Sivana's weaponry shoots what is described as a "fiendish paralyzer ray", echoing his comics counterpart's use of the artificial element "Suspendium" to trap the Marvel Family (and, accidentally, his own) in suspended animation for twenty years.
In "The Golden Age of Justice", Batman uses Per Degaton's Spear of Destiny to temporarily de-age the JSA, and Degaton says he'll send them to Valhalla. In Post-Crisis continuity, the reason the JSA weren't quite as old as they should be was that they'd spent years in a dimension based on Norse mythology where they didn't age.
The cold open of "Time Out for Batman!", which has Batman team up with the Creeper to defeat Hellgrammite, is a loose adaptation of The Brave and the Bold v1 #80. This, incidentally, makes it one of very few stories based on an issue of the original comic.
In the end of "Night of the Batmen" one of the alternate dimension Batman clones is Terry McGinnis, which in turn could possibly mean that this is an alternate Earth in the DCAU multiverse.