The Death Traps on display in the Batcave's "Joker Wing" were taken from the original Adam West TV series.
In "Night of the Huntress!" the Batmobile transforms into what looks very much like one of the Bat-Knight robots from Kingdom Come.
Speaking of giant robots, the one female member of Babyface's gang just happens to end up in a yellow exoskeleton.
The show continues the trend of the comic by having streets or place names in Gotham and Bludhaven named after influential Batman writers and artists. In "The Color of Revenge!", Batman mentions the intersection of Haney and Aparo, a reference to the writer and artist of the original The Brave and the Bold comic that heavily influenced this show.
"Legends of the Dark Mite!" is one giant Shout-Out episode, including but certainly not limited to:
The title is a massive mythology gag referencing primarily the BTAS Legends of the Dark Knight which itself references the varying portrayal of Batman over the years.
Among other Batman fanboys at a convention held by Bat-Mite is one is a Batman costume identical to the one worn by Hank Venture. Which itself was based on a real-life Batman Halloween costume sold in the late 60s and the 70s.
Bruce Timm and Paul Dini (creators of the DCAU) are also present at the convention, in costume as the Joker and Harley Quinn (well, Harley WAS Dini's creation!) respectively. For added humor, Dini actually wrote this episode.
Bat-Mite ends his episode like an old Looney Tunes cartoon, waving and saying "That's all, folks!" while the Looney Tunes theme song plays. Weirdest Shout-Out in a Batman show ever.
That's NOT all — Bat-Mite also gives a shout-out to Bewitched, wiggling his nose to disappear at the fade-out. Earlier, to transform into Batman, he crosses his arms and nods his head a laI Dream of Jeannie. Paul Dini also wrote the admitted Bewitched homage episode This Little Piggy for Justice League Unlimited.
Bat-Mite's description of Batman as a tortured avenger "crying for mommy and daddy" is an Ironic Echo of one of The Joker's darkest lines in Batman Beyond: Return of the Joker used to emphasize the differences between the Brave and the Bold version and the Animated Series version of the character.
Dick Sprang-inspired designs for Two-Face, Catwoman, Penguin, Joker, 60s Mr. Freeze (or Mr. Zero, as he was called then)... The list goes on and on.
Dr. Canus' attire from "The Last Bat On Earth!" looks awfully similar to a certain Scruff McGruff, complete with green trenchcoat.
Bane's first appearance on the show had him lifting Batman up just like he was about to break his back over his knee like he is famous for doing in the comics. Luckily Wildcat was there to save Batman.
The theme song itself could arguably be inspired by "Tank!" the Cowboy Bebop opening.
In "The Super Bat-Man of Planet X!", Rothul's combat robots look uncannily like the Fruit Fucker 2000.
Beloved DC humor characters Sugar and Spike appear in the comic as allies of a de-aged baby Batman. The same issue also features a time machine that is best known to fans of Superdickery as Lois' time travel popemobile.
In "Mayhem of the Music Meister!", Calendar Man is seen strapped to a dolly with a muzzle over his mouth like Hannibal Lecter, probably in reference to the Lecter-inspired portrayal of him in The Long Halloween.
The Music Meister's frequent costume changes involve homages to (among others) KISS, the Phantom of the Opera, Elvis Presley, Liberace and Elton John. They also reference various types of music, from generic band geek to techno to opera.
Adam Strange's leitmotif in "Mystery in Space!" features heavy electric guitar noodling, deliberately evocative of Queen's soundtrack for Flash Gordon.
In "Hail the Tornado Tyrant!", Red Tornado's son is called Tornado Champion and Tornado Tyrant, both nicknames Red Tornado had over the years. Likewise, Champion's design before his Face-Heel Turn resembles Red Tornado's original look in the comics.
The "Batman doesn't eat nachos!" line in "A Bat Divided!" definitely seems to be a reference to one of the nitpicks fans made about an early episode of The Batman, which showed Bruce eating nachos in the Batcave. Not to mention, the cheese sauce Slacker!Batman pours on his nachos has a picture of Little Cheese on it.
The sound effect Starro makes is the same sound as Martian ships from the 1953 film adaptation of The War Of The Worlds. The Faceless Hunter's narration in "The Power of Shazam!" of how Starro identified Earth as its target is a shout out to the open narration of the film as well.
In "The Siege Of Starro" Part I:
There's a moment the screen freezes for a second. This is to showcase an homage to the cover of the issue of The Brave and the Bold (the original comic) where the Justice League debuted, fighting— Starro!
The Haunted Tank cold open is basically a two-minute episode of The Dukes of Hazzard. Right down to the slo-mo jump and car horn that plays "Dixie."
During "Requiem for a Scarlet Speedster!", Barry Allen and Professor Zoom duel while running at super speeds around the world - at one point they pass through a suspiciously familiar stylized desert, and their "superspeed" sound effects briefly become the same as the one used for The Roadrunner.
The same episode has what is arguably a Mortal Kombat vs. DC Universe reference as Zoom and Allen fight each other in free fall, each attempting to turn the other into the fall in the same way Free Fall Combat worked in that game.
While the Harley Quinn in "Emperor Joker" looks more like a Roaring Twenties flapper (she is probably based on silent comedienne Mabel Normand), when Joker puts Bat-Mite into a Jester outfit, it's the Jester outfit the classic Harley wore in her original Batman: The Animated Series appearance.
During the museum scene, in the background is what appears to be a bust of a generic male from The Far Side.
When the newly-powered Joker transforms into a skin-tight spandexed emperor with a Whoopee Cushion crown, he raises his arms and shouts, "I'm the king of the world!" just like Jack does in Titanic.
Towards the end of "The Color of Revenge!", the mostly red-clad Robin takes down Crazy Quilt's blue-clad, bald and BFG-wieldingMook with a stick. Say it with me - BONK!
In "Game Over For Owlman!", the apparent references to The Killing Joke in "Deep Cover for Batman!" are subtly confirmed when the Joker uses the words "killing" and "joke" in quick succession.
In "Emperor Joker" there's a blink-and-you'll-miss-it reference to The Tick - during the "Where's the Fun in That" sequence, a gigantic Joker can be seen walking through the city, while the buildings around him burst to life. One of them sports a face and "teeth", like the buildings, that Tick hallucinated in one of the episodes. Those buildings can be clearly seen in the intro to the show.
The iconic Hindu poster from Watchmen (most prominently seen in the "Fearful Symmetry" chapter) is very briefly shown in the Doom Patrol episode.
In "Gorillas in Our Midst!" Gorilla Grodd ties Batman and Detective Chimp into the infamous crotch-laserdeath trap.
The episode's title is a pun on the movie Gorillas in the Mist.
In the opening for "Triumvirate of Terror", Batman's Rousing Speech to the Justice League mentions "little Julie Schwartz and Frankie Miller from Gotham".
The end of the episode jumps 50 years into the future; Batman is gray-haired, wearing what looks like an exoskeleton, and riding in a motorized wheelchair. The reference is completed when the chair transforms into the armored Batsuit from Kingdom Come.
Part of the fight between Superman and Batman is based scene-for-scene on the final episode of Justice League Unlimited and its Superman/Darkseid fight (the bit where Supes punches Bats through a building, superspeed-intercepts him on the other side, and then smashes him down into the ground).
The other part? The final fight in The Dark Knight Returns. Batman's armored suit is an obvious visual reference, but the still shots of Batman hitting Superman seal the deal, as they are directly lifted from the comic.
The other other part? The brawl between Batman and Superman actually mimicked Superman's climactic battle with Darkseid in Justice League Unlimited.
The main episode opens with a shout-out to "Jimmy Olsen's Death-Trick". Except Superman has to attend to an emergency before he can say he's Clark Kent, and just before he leaves, he reveals that Jimmy's act didn't fool him one bit, as he found him to be perfectly healthy with his X-ray vision.
The identity of the Robin in the teaser is unknown, since the last time he appeared he switched over to Nightwing. It may have been meant as a flashback, or it's a new Robin.
When Superman throws Krypto into space, the scene looks very similar to one in Underdog.
Aquaman's Rousing Song Of Heroism mentions wallcrawling among the many superpowers possible. The guy he's dressed as is the Tarantula, a Golden Age hero retconned into a Spidey knockoff in Roy Thomas' All-Star Squadron.
In "Powerless", the setup for Captain Atom's Public Service Announcement is taken straight from G.I. Joe.
In The Eyes of Despero, Batman lays out Guy Gardner in a nod to a classic scene from Justice League International, complete with G'nort providing the "One punch! One punch!" line.
The voice of Batman's talking street luge in Mitefall is an obvious impression of William Daniels as KITT from Knight Rider.
The premise of the episode is Bat-Mite trying to get the show canceled by having it Jump the Shark (explicitly using that phrase, even) as Ambush Bug tries to stop him. Ambush Bug is voiced by Henry Winkler — the original Shark Jumper, Fonzie from Happy Days.
In the episode "Bat-Mite Presents: Batman's Strangest Cases!"
It features Scooby and Batman dual-punching the Joker after Bat-Mite uses his powers to allow violence.
The conference table for the Monster Society of Evil in "The Malicious Mr. Mind!" reveals that the organization has the exact same logo as the United Underworld from Batman: The Movie.
In "Emperor Joker" Bat-mite in Fourth-Wall Breaking fashion, brings up The BTAS episode, The Laughing Fish. And the comic A Death in the Family even saying that he voted in whether Jason Todd would live or die. (He wouldn't say which he chose) this being the first time Jason Todd was name-dropped in a Batman cartoon.