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That statue that Drake Mallard pounds on to start his chairs flipping, sending him and his allies to Darkwing Tower? It's Basil from The Great Mouse Detective. Character designer Toby Shelton helped designed the casts of both.
Not only that, the idea of a statue opening a Secret Passage to a superhero's headquarters is a reference to the William Shakespeare bust that opened the Batcave passage in the 1960's Batman series.
DW's costume is a dead ringer for DC Comics's Crimson Avenger, one of the first costumed heroes, or perhaps to the (first) Sandman, another DC hero with a similar costume (at first) and a gas gun.
The episode "Aduckiphopia" (besides referencing Arachnophobia) had DW grow four extra arms (something that once happened to Spider-Man) and had him take the new identity of 'Arachno-Duck' (wearing a variation of Spider-Woman's costume.)
The episode "Planet of the Capes" was a shout-out to normalman.
"Stressed To Kill" has a "How To Relax" segment in the style of the classic Goofy "How To _____" Disney shorts.
"Film Flam" in addition to all the classic film references (being a Tuskerninny episode, after all) also has this exchange:
Gosalyn: "Look dad! It's Mongol from Mars!"
Darkwing: "Yeah, right! And I'm Donald-" (sees the Martian monster about to attack) "-DUCK!"
There were also at least two references to The Far Side. "Beauty and the Beet" had Dr. Bushroot's fellow scientists Dr. Gary and Dr. Larson, while "Twin Beaks" featured a group of alien cows from the planet Larson. ("On The Far Side of the galaxy.")
And the first arc of the comic revival is called "The Duck Knight Returns."
And one of the alternate covers for the first issue is of Darkwing getting spooked by the lightning bolt that was on the Cover for The DKR.
Upon being knocked dazed and stupid from a nasty fall, Darkwing proceeds to sing Simon & Garfunkel's "Mrs. Robinson."
An averted shout-out: In the original drafts of the show, Darkwing was a spy (the series was conceived as a James Bond parody) and all the villains were members of the FOWL organization. In the actual series, only a couple of them are. The FOWL mooks are called "Eggmen," and originally their commander was meant to be Tuskernini, who is a walrus. In the final show, Tuskernini is not a FOWL agent, so the eggmen and the walrus never meet.
The very first villain is named after Taras Bulba, a Russian novel and movie starring Yul Brynner. This is quite possibly the most obscure reference in the Disney Animated Canon.
The episode "Merchant of Menace" featured a villain named Weasel Loman.
How about Tuskernini? They probably just chose the name for the "tusk" pun, but he isWicked Cultured nonetheless. The name's a Shout-Out to Arturo Toscanini, an Italian orchestral conductor known for intensity and perfectionism.
The ending of the episode "Dead Duck", from the moment when DW on his knees promises to Death "to be good" begging for a second chance and especially after his wake-up, with his joyful cries "There's my couch, there's my chair. There's that rug I always trip over, I love that rug!", is a quite clear allusion to Dickens' A Christmas Carol.
In "Getting Antsy" the villain who shrinks the city is named Lilliput and a couple of germs are named Blob and Ray.
Issue #4: In the near-final pages when Scrooge McDuck is explaining how he plans to restructure Quackwerks and help rebuild the economic and law-enforcement aspects of St. Canard, there are portraits in the meeting room that show crude caricatures of Mickey, Donald, Pluto, the three nephews, and Scrooge during past adventures.
Issue #5: In the prison, with Bushroot, Megavolt, and Quackerjack (who seems to have a scowl permanently replacing his toothy grin so far), is a single Beagle Boy, and off-panel with just his ear and stubbly cheek, is none other than Big Bad Pete. Later, in a flashback, there's a bear-skin rug that resembles old-timey character Br'er Bear.
In issue #6: Gosalyn can be seen carrying a The Incredibles lunchbox if you look closely. One of the plant sculptures is Pinocchio.
Not to mention that Negaduck is standing on top of Goliath from Gargoyles on the very first page. And one of the protester's signs was "Bring back Bonkers!"
When DW presents himself to the crowd, a group of Darkwing Duck fangirls looks up at him. They're all dressed like the Disney Princesses (and Alice.) Two pages later, another female character is wearing a T-shirt with Animal on it.
It also combines this with a subtle Crossover Punchline with a dazed Steelbeak saying "Ma? That you? I will watch my language... Buster told me to." Both Fowlmouth and Steelbeak were voiced by Rob Paulsen in the cartoons.
Issue #17 (leading into Ducktales #6), during the Ducktales crossover. Scrooge and his nephews are helping Darkwing investigate a strange ink that can mutate normal people into monsters. At the end of the issue, Honker and Scrooge's nephews fall into the stuff and turn into classic giant Disney villains: Honker becomes Willie The Giant, Huey becomes Chernabog, Louie become Maleficent (as a dragon), and Dewey turns into Monstro.