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 own 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. Or to some versions of The Green Hornet, whom Crimson Avenger was a Captain Ersatz for in the first place.
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, while another had him mimicking Batman's leaping pose.
Im "Star Crossed Circuits", 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.
When Bulba grabs his henchman Hammerhead by the neck and reminds him of his stooge status, Hammerhead replies with "Yes, boss. I'm a stooge. Just call me Curly."
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.
Earlier in the episode, when Launchpad asks to stop for a burger (or three), Darkwing complains by referencing The Lone Ranger;
Launchpad: Hey, 'ya burn a lot of calories thwarting evil.
Darkwing: Fine. Lovely.
The pair march off-screen
Darkwing: (as he walks): I'll bet Tonto never made The Lone Ranger stop for burgers!
In "Slime OK, You're OK", when the giant patch of ground is brought to life by Bushroot's IQ2U potion, she first references Mae West's most famous line from She Done Him Wrong with "Why don't you come up and seed me some time?"note Also a Beam Me Up, Scotty!, as West actually said "Why don't you come up some time and see me?", then Greta Garbo's most famous line from Grand Hotel with "I vant to be a lawn," complete with vocal impressions of West and Garbo.
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 Br'er Bear.
One of the mishaps inadvertently caused by Morgana has her accidentally bring the Thunderquack to life. It yells, "Feed me" at Launchpad.
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.
The scene where the different versions of Darkwing attack Negaduck possessed by Paddywhack resembles the iconic scene from Crisis on Infinite Earths where all the DC superheroes are fighting the Anti-Monitor.
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.
One cover features Launchpad and Morgana standing in front of a set of posters similar to Days of Future Past.
Issue 13 has Thomas O'Malley seen eating a fish skeleton while sitting on some trash cans and Br'er Rabbit appearing on a poster reading "Have you seen me?".
One of the things that Carmichael Q. Anthony throws is a Dalmatian from 101 Dalmatians.
When Carmichael Q. Anthony is given his coat with pockets full of various objects, a Goofy PEZ dispenser can be seen. When we see said objects embedded into the wall, forming Darkwing Duck's face, The Genie's lamp and Mickey's sorcerer hat can be seen.
The third panel One-Shot appears in features him holding a Wii Remote.
One of the panels where Darkwing fights One-Shot has framed portraits of Goofy, Panchito, and Jose Carioca, though the top parts of their faces are obscured.
In issue 14, one of the new super-powered villains Darkwing has been fighting appears to be Stitch.
In the flashback where Mortimer L. Marquand explains how he became Cat-Tankerous, Max, PJ, and Pistol can be seen in the panel where Mortimer is looking longingly at Gosalyn in class.
Scrooge McDuck and the snouts of Goofy, Clarabelle Cow, and Horace Horsecollar can be seen on Suff-Rage's viewing monitors.
The beginning panel of the 15th issue has a cameo by Tito.
Toby can be seen with Darkwing propaganda materials on him.
One of the alternate covers is a parody of the Obama "Hope" poster that depicts Launchpad and reads "Crash".
Issue 16 features a page that has posters featuring the Monsters, Inc. and The Mighty Ducks logos and cameos by Jiminy Cricket and Oswald the Lucky Rabbit.
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.