- The second-to-last scene of "The Fowl Friend" is nearly a word-for-word copy of the second-to-last scene of The Iron Giant. It's then repeated in a later episode just to rub it in.
- Porky's nephews and niece in "Pig Planet" are Expys of Yakko, Wakko and Dot. Rob Paulsen, Jess Harnell and Tress Macneille (the same voice actors) were brought in to provide voices for Porko, Puerco and Sow.
- In the MMORPG episode, Daffy transforms into Beaky Buzzard, Axle Gator, and Muttley.
- And we can't forget: "Samurai Quack"
- Including the main villain being a near-perfect expy of Aku, down to the same voice actor, the now-late Iwamatsu Mako.
- Samurai Jack creator, Genndy Tartakovsky, also provided a short cameo for that episode.
- In the episode "Green Loontern", itself a shout out, a shot of the captured members of Green Lantern Corps has a brief cameo of what appears to be Mortal Kombat's Raiden (which becomes hilarity in hindsight after Mortal Kombat vs. DC Universenote ).
- In "Attack of the Drones", the Great Gazoo, Commander Worf, and Dr. Zoidberg appear as members of a council at the beginning. You can even hear Zoidberg say "So what do we do?" if you listen closely, since Billy West was already Porky Pig on the show.
- There's also The Fudd.
- From the eponymous episode, the Cadet gets the idea to sneak them in by disguising themselves as the guards. When asked by X-2 if this plan will work, the Cadet answers that he's seen it work before. When asked by Dodgers where he's seen it work, he answers, "The Wizard of Oz."
- In the same episode, there's a reference to the original short, where Dodgers and X-2 argue over who's claiming an asteroid for their planet.
- In "K-9 Quarry" Marvin and K-9 are on a hunting trip and end up being hunted down by Wile E Coyote in a Predator suit. His trophy room is also filled with various Hanna-Barbera cartoon characters.
- The Martian Commander has a lot more in common with Zapp Brannigan than just his voice actor...
- In "The Trial of Duck Dodgers", Dodgers is about to bombard a Martian ship and "has only one pass at this." The Cadet tells him:Cadet: T-t-trust your feelings, Captain.
Dodgers: Nah, I'm pretty sure I'm gonna use this expensive targeting computer.
- One episode has a space prison called "Wantannaguannamo Bay".
- The end of one episode has a spurned Martian Queen shooting up mechanical dummies that look like Duck Dodgers, and drops the line: "So they're mechanical!" (with a connotation of "So what?") This is a reference to the end of the Bugs Bunny episode "Hair Raising Hare", where Bugs says this about a mechanical female rabbit.
- The episode "The Mark of Xero" is a shout out to both Zorro and Daffy's previous role as The Scarlet Pumpernickel.
- The intro began with the famous Looney Tunes rings.
- And the ship-chase at the end of the intro is very similar to the chase at the end of the intro to Blake's 7.
- In "Til Doom Do Us Part" the introduction of the Legion of Duck Doom is an exact copy of the opening credits to Challenge of the Super Friends.
- Queen Tyr'ahnee, in appearance and in name both, is suspiciously Drow-like.
- The nebula battle in "The Queen is Wild" has moments that are taken shot for shot from Star Trek II: The Wrath of Khan.
- In another episode, we have a rapidly aging Dodgers and Cadet walking around to a tune that sounds like a dead ringer for The Odd Couple theme.
- Another famous Loony Tune is referenced in "Of Course You Know This Means War And Peace pt. 1":Queen Tyr'ahnee: Of course you know...this means war!
- The exchange between X-2 and Dish in "Of Course You Know This Means War And Peace pt. 2" is taken from Kill Bill.
- The segments from season 1 episode 8 are named for Star Trek II: The Wrath of Khan and the Star Trek: The Original Series episode "Spock's Brain."
- When Z-9 orders Counselor Dish to eliminate Marvin, she replies with "By your command.", mirroring the inflections of the Cylon Lucifer from the original Battlestar Galactica.
- In one episode, when Dodgers is on a 'villain' kick, the Space Cadet is saddled with the name "Chaos Boy" and his Fan Disservice uniform consists mostly of a hood with the Chaos Star on it.
- When Dodgers runs out on the Martian Queen in "To Love a Duck", he says that it wasn't meant to be, but "we'll always have Paris".
- In one episode, Kelly Ripa stars as a Stalker with a Crush and then a scene from Fatal Attraction is referenced when a frightened Dodgers and Cadet find a pot full of rabbit stew simmering in the kitchen.
- Dodgers and Cadet are trying to use a small ship to evade defenses built around a full scale assault. Lampshaded by Commander X-2, "How many lives must that accursed movie claim?" Evidently, it wasn't the first time someone tried it either, as a Martian Centurion told the Commander what Dodgers was attempting, his response was, "What, again?"
- The episode "Deathmatch Duck" is a Whole Plot Reference to the Star Trek: The Original Series episode "Arena" in which Captain Kirk fights the Gorn on Cestus III.
- Also, Dodgers being promoted to Admiral in "Of Course You Know This Means War and Peace", only to end up demoted back to captain, is exactly what happened to Kirk.
Shout Out / Duck Dodgers