The most obvious Disney example, cited in the quote on the main page: Mickey Mouse is an anthropomorphic mouse. His best friend Goofy is an anthropomorphic dog-man who walks on two legs. Mickey's pet Pluto is a (relatively) normal dog that mostly behaves like a real dog.
This is parodied on Drawn Together, during a montage of hostage situations. One of those situations is Pluto holding a gun to Goofy's head screaming, "He's the only fucking dog who good enough to wear fucking pants? Well, I want to wear the fucking pants for once!" (before casually shooting Goofy and then himself)
A comic strip also made fun of this: A cartoonist makes a strip in which the main hero is a "mouse", his best friend is a "dog" and his pet is also a dog. Said strip is rejected for lacking consistent internal logic.
In some theatrical cartoons, Goofy owns a pet dog. He is also, for some reason, identified as George G. Geef in these cartoons, and his floppy dog-ears are not visible. A short film, "The Goofy Success Story", played with the Animated Actors trope by showing Geef as a role that Goofy played as an actor.
A notable Lampshade Hanging occurs during a Goof Troop episode in which, Goofy, when confronted by a pair of vicious non-anthro canines, says something to the effect of: "I'm great with dogs. It's like I'm one of the family".
Also in Goof Troop, Goofy had a pet cat, and Pete had a pet dog. While Pete was originally a cat, his later appearances suggest he's a dog or maybe a wolf. And then there are a number of similar but separate characters existing in a number of mutually exclusive universes and a whole bunch of cartoon shorts that have Negative Continuity anyway. There are even multiple Petes running around the DuckTales universe.
In another episode of Goof Troop, Goofy hears a crash in his garage and assumes it was made by a giant mouse. Aside from a quick cameo in A Goofy Movie, Mickey never appeared on Goof Troop, but...
A 1930s cartoon Mickey's Good Deed, has Mickey playing Santa Claus to a family of poor cats — smaller than him. Pete is apparently the absentee father, as there's a picture of him, in prison stripes, on the wall. You can tell they're poor as their empty cupboard is overrun with mice. Tiny, non-anthro mice!!! And why the cats just don't eat them is never addressed.
In the cartoon Society Dog Show, Mickey is the only non-dog Funny Animal to take his dog to the dog show. Everyone in that cartoon is a dog anthro... judging non-anthro dogs.
On the subject of Pete's wife: Most "people" in Disney comics are depicted as very anthropomorphic dogs. They have a black nose and (sometimes) floppy ears, but are otherwise human. Even real historical people (similar to Arthur). Which makes Goofy even more confusing as he looks nothing like the other "dogs".
Disney animators have given them the nickname "Dog-Noses", a term usually applied to the extras walking around. The creator of Goof Troop and Quack Pack introduced this term in an interview where he talked about both shows. Originally, he intended to have humans — just ordinary humans — inhabit both shows. However he was overruled with Goof Troop, and forced to people his universe with dog-noses. He was successful later on with Quack Pack though. Had he been allowed to use humans in both as he intended, Goof Troop and Quack Pack would have shared the same universe, much the same way Duck Tales and Darkwing Duck did.
Point of Order: in the original Goofy-specific cartoons, EVERY extra was a Goof, extremely similar to Goofy himself but each being slightly different. This was carried over into more modern material as well; if Goofy was the main driving force of the feature, everyone in it would be a Goof.
Regular ducks have been shown to exist alongside the anthropomorphic Donald Duck. Adding to the weirdness parade, in a theatrical cartoon, Donald once encountered a recipe for roast duck in a cookbook, which he angrily ripped up. In a different cartoon he heard another recipe for it on a radio cooking show. His only comment was "Over my dead body".
And the Carl Barks comic "The Gilded Man" shows Donald and the nephews being quite shaken and disturbed by the sight of stuffed normal ducks sitting on a shelf. This is quite unusual as most Barks stories treat the Ducks as stand-ins for humans, and this is, in fact, one of the only times they seem to recognize their relation to non-anthropomorphic ducks, other than the times Barks has them refer to "us Ducks and humans"...
In Fantasia 2000, pictured on the main page, Donald appears as a deckhand on Noah's Ark, responsible for a group of animals that includes, to Donald's visible puzzlement, a couple of normal ducks. Best Lampshade Hangingever.
One particularly Nightmare Fuelerrific Donald Duck comic strip had him going duck hunting. Like this one. The "confusion" part in "Furry Confusion" is especially apparent in panels 2 to 4. In the picture, the ducks seem to notice him in passing as well.
One comic had Scrooge hypnotized into buying all the items in the song "The Twelve Days of Christmas" (don't ask), giving us some awkward scenes with French hens (Clara Cluck?) and geese (Gus Goose?).
Lampshaded and twisted in an episode of Darkwing Duck. Steelbeak (a Bond villain-ish anthropomorphic chicken) turns downright Hannibal Lecter with the line, "I'll offer you my recipe for roast chicken."
Spoofed further in the 2010 Darkwing Duck comic book. Goslyn is at a pet store when she notices an area full of baby ducklings. "Okay," she says, "this is just creeping me out."
In an early MAD parody of Disney by Harvey Kurtzman, "Mickey Rodent" traps his rival "Darnold Duck" naked in a zoo. The story ends with the zoo staff (human, of course) marveling over the "mutation freak" that "almost sounds" as if "it's" screaming "Get me back my clothes!" The last panel shows poor Darnold, his modesty covered with leaves, surrounded by non-anthropomorphic ducks, and facing a possible taxidermal fate because "it is, after all, only a duck."
The Gran Festival starring The Three Caballeros ride at Epcot has a moment like this. Like its source material, the videos combine animation with live action. Looking for Donald, José and Panchito ask a live action chef if he's seen a duck. They quickly realize that they don't want to know the answer to that question, and run off. Another version of the scene has the chef showing them a plate of roast duck, which gets a similar reaction from the duo.
Lampshaded at last in The Mighty Ducks animated series, where two of the eponymous anthro ducks (from another universe) spend the end of an episode discussing the differences between themselves and Earth ducks.
There is also an old story somewhere where Donald, his nephews and Scrooge meets some native indians where one of them is asked by another to describe what a duck is. Cue the indian mimicking that ducks can fly and float on water, to which our gang are left with dumbfounded reactions and asking if he's joking.
With all of this in mind, The Lion King level in Kingdom Hearts II is just a carnival of Furry Confusion. Donald is temporarily a non-anthro bird who can fly and Pete is a non-anthro cat (more specifically, a lion). What makes it worse is the fact that Donald comments on Sora's transformation (into a lion) while avoiding any mention of Goofy's or his own. It should be mentioned that Donald's non-Anthro form is identified, in the Kingdom Hearts literature as "Bird Donald". Try to read that without having a Psychic Nosebleed.
Speaking of Disney ducks, DuckTales gave us at least two episodes with some good examples of Furry Confusion:
In the episode inspired by The Odyssey, the Odysseus stand-in, his girlfriend, and most of the supporting cast are Dog-Noses. Circe, of course, turns several of them into non-anthro pigs. Later, Circe herself is turned into a pig as punishment. Here's the thing: Circe was depicted not as a dog-nose, but as an anthropomorphicpig. Uh...huh?
Even funnier is the episode where Launchpad finds himself the unwilling object of affection for a trio of harpies. And the harpies were birds with human heads. And so we got to see birds with some human features fawning over a human with some bird features.
DuckTales also introduced a new sidekick for Scrooge's nemesis Magica De Spell; her brother Poe who was the subject of a Baleful Polymorph. Specifically he was turned into a... bird. A different species of bird (he is a raven now), to be fair, but still... a bird. He can still talk, he still wears clothes (a hat at least), he still has functional Feather Fingers, and is for all intents and purposes the same character just a different species. Still, he views his fate as awful and wants to turn back into a duck. This despite the fact that he merely seems to have gotten a bit shorter and can nowfly (heck, ask an ornithologist and they will make a good argument that duck-to-corvid is an upgrade). He's just barely less anthro than the other characters.
Then there's the Mickey Mouse cartoon, "The Worm Turns". Mickey is working on a courage potion and goes around testing it on a variety of non-anthropomorphic animals — including a normal mouse. Things also get pretty awkward whenever Chip and Dale appear in the same cartoon as Mickey.
Regarding Mickey/Minnie and mice, there's the page image of Eek, a Mouse!!, and this weird Look comic about medication, where Mickey tests the drug on lab mice.
Speaking of Chip and Dale, there's an episode of Chip 'n Dale Rescue Rangers where Dale wants to get a pet. His desired pets, a frog and a kitten, are fairly standard for a human. But considering his other best friends are mice and a fly, the wisdom of bringing them home is... questionable, never mind the sight of Talking Animals having pets. (Not to mention the logistics of getting them up into a tree all by himself.)
The kitten is the worst, as other cats in the series (Fat Cat for example) are portrayed as being every bit as anthropomorphic as the titular rodents. It's almost like wanting a human baby for a pet.
The confusion goes up about eight or nine more levels when Dale discovers an unusual-looking chipmunk-sized animal lost in the park and, because he acts just like a dog, Dale decided to make a pet out of him. Said animal soon reveals that he can talk, that he is an alien, and that he is a miniature Stegosaurussent from the Dinosaur Planet to check on the team of explorers who went to visit Earth 155 million years ago. And it turns out that those small explorers became some of the dinosaurs we know when they started eating Earth food; when our hero does this he grows very large and loses his ability to speak. Things get straightened up eventually and the alien returns to his ship to go back home, but not before topping off the Furry Confusion bonanza with this line:
"I'd love to take you with me, Dale. But I'm not old enough to have any pets."
You think this is bad? Chip 'n' Dale live in the same world as Donald, as shown by several episodes. However Rescue Rangers takes place in the world of Humans, not Anthro-animals, Humans, which shown by the Pilot and a few others. However Rescue Rangers still live in the same world as say, Darkwing Duck (as shown by one issue of its new comic book). So question is - where do humans go during different shows?
Of course, see the Quack Pack example above...Donald does have humans in his world...sometimes.
What humor there is in Chicken Little derives from lampshading this trope. For example, a father and son play Frisbee in the backyard, and the son catches the toy in his mouth — they are both Funny Animal dogs.
Then there is the egg-shaped rug in Chicken Little's bedroom. No, not a whole egg. A broken egg. Yolk and all. (Classic "fried egg"-style eggs are non-fertilized so it's not quite the same thing. Still pretty squicky though...)
Pinocchio evidently takes place in a universe with fully anthropomorphic cats, foxes, and crickets; ordinary cats and fish with human-like awareness; and fully non-anthropomorphic animals. The closest this comes to furry confusion (imagine if Figaro met Gideon!) is how Cleo doesn't seem to have a problem with the fact that all Geppetto and Figaro seem to eat is fish.
Bronx and the other "gargoyle beasts" like him in Gargoyles are kind of an odd, borderline case. At first glance, Bronx is a wingless Gargoyle, and isn't really any physically different from the talking Gargoyles aside from lacking wings. But he acts like, and is treated as, a non-talking, non-loincloth-wearing animal. A few episodes (such as the one that introduced Puck) explicitly pointed out that he was the other Gargoyles' "dog", while the show's creator described him as their equivalent of a non-human ape.
In their early cartoon appearances, Clarabelle Cow and Horace Horsecollar were sometimes shown as regular four-legged non-clothed barnyard animals, and other times as fully anthropomorphic creatures on par with Mickey, Minnie, Donald and Goofy.
Horace's first appearance was as a horse that Mickey was riding. At other times, he has been depicted himself riding non-anthropomorphic horses.
There's even a story where he sees a contest for whoever can get a Parrot to say "Rio De Janeiro". He decides he's going to enter this contest. He then goes out and buys himself a Non-anthropomorphic parrot!
In TaleSpin, all the characters are anthropomorphic animals. There are also non-anthro, non-sapient animals including normal-looking sea life and a few "cryptids". Where it gets really weird, though, is the episode that features a talking parrot who clearly has full human-level intelligence — but is not anthropomorphic and is treated like a pet by all the other characters.
The show gets even weirder when you consider the source material. Baloo, Louie and Shere Khan were characters from Disney's The Jungle Book, and were pretty anthropomorphic to begin with. Suddenly it's the 1930s, and the same characters are wearing clothes, flying planes, etc. Their designs changed a bit as well; Baloo traded his claws for fingers, but otherwise looked the same. Khan on the other hand went from a quadruped to a biped, a much more noticeable change.
Diabolical Mastermind Thaddeus E. Klang from the "For Whom the Bell Klangs" two-parter seems to be an anthropomorphic cobra (albeit with a metal jaw and hands), just as smart as everyone else. Except the end reveals he's not anthropomorphic. As no one else witnesses this, it seems to serve no purpose but to confuse the audience.
In the Disney story Panchito, Panchito only realizes he's left behind Clara Cluck when he's served a plate of Roast Chicken. He immediately goes out to find her, and no one questions that a Rooster was just served a Roast Chicken.
A running thing in the comics was that Brer Fox and Brer Bear were after various animals (Chip, Dale, Bambi, etc) sometimes to eat them and sometimes to sell them to a pet store. This slightly works since the Brer's are more humanlike and actually live in houses and wear clothes. However, one comic has Brer Bear getting so mad at Brer Fox that he ties the fox up and takes him off wanting to sell BRER FOX to a zoo, despite the fact that both Brer's are closer to people than they are animals. So are humans still the elite in the Disneyverse? Can animals willingly sell each other? Who would want Brer Fox, any way? Many, many, many questions are raised.
In a similar vein, Handy Manny has his "team" of sentient, talking tools (who are just barely anthropomorphic, in that they resemble regular tools with eyes and mouths but no limbs — how they move or grab things is a mystery), yet their universe also includes regular, non-living tools. In the opening title sequence, two of the tools paint a sign using non-living paintbrushes.
Minnie Mouse has a cat named Figaro in some shorts of House of Mouse. A joke from the writers, maybe?
House of Mouse is definitely one of the worst offenders ever. At one point, we actually get to see Baloo (a talking, bipedal bear that is completely naked) sitting next to Little John (a talking, bipedal bear that wears a hat, a tunic, and shoes, but no pants), and at another, we actually see Jiminy Cricket (a talking, bipedal cricket that wears clothing) sitting next to Cri-Kee (a nontalking, quadrupedal cricket that is completely naked).
This is addressed, indirectly, in the episode, when Donald temporarily dubs himself "Donald Donkey" as "Donkeys can't fly", indicating that he internally knows that, as a duck, he should be able to fly.
The "what is Goofy" question is lampshaded in House of Mouse. Hades calls Goofy over to complain about the menu using his name without authorization, then gets derailed by asking what Goofy is supposed to be.
To add insult to injury, he is flying an airplane rather than flying like a normal duck alongside the other ducks. The only time Donald is actually shown flying like a normal bird is in one later scene in The Three Caballeros, but he is flying like a hummingbird.
Also, Ludwig Von Drake is shown flying using an inflatable jumpsuit rather than like a normal duck.
In another Mickey Mouse Clubhouse episode, Donald is shown swimming like a dog or human as opposed to like a duck.
Applying Fridge Logic to the Toy Story films generates a certain amount of Toy Confusion. Just what constitutes a "toy", anyway? The Etch-A-Sketch is animated and sentient, but Molly's iPod doesn't seem to be. Toy vehicles are self-propelling, but toy versions of other objects (xylophones, tracks for toy trains) have to be put in place by the humanoid toys. The L.G.M.s who worship "the Claw" are sentient, but "the Claw" itself (basically a big toy with little toys inside) is not.
However, at the end of the first movie, Woody drives RC Racer against his will with his remote control to rescue Buzz.
Off of that, RC is considered a sentient toy. In the sequel another toy car (possibly a Barbie car) can be driven by the toys, but gives no indication of being sentient.
Not to mention Bullseye, a toy horse who acts like a horse (and dog), despite the presence of other animal toys who speak and act normally.
Another Pixar example would be that aphid (which is treat like a pet dog to the ants) in A Bug's Life.
Or Bessie (a non-anthro bulldozer) from Cars. And in the Cars universe, there are insects that resemble VW Beetles, as well as farm equipment that behave like cattle. And in one of the spinoff shorts starring Mater as a bullfighter, there are bulldozers that also act like cattle similar to the farm equipment in the movie.
In the sequel, there are tiny airplanes that act like birds, and one of the racers' crew chiefs is a VW Beetle! (in the first film, VW Beetles are all supposed to be the car equivalent of insects)
Back to the first Cars film, there is actually still a dinosaur on the logo for Dinoco, and one RV seen near the end of the film appears to be surrounded by plastic flamingos, while another has a jackalope tattoo on his rear end!
A trailer for Disney Infinity has Mater trying to strike a conversation with a non-anthropomorphic vehicle.
The Brave Little Toaster: Although all electronic devices are sapient (though the humans don't even realize this), the junkyard cars are all sapient as well, but the Master's car isn't (probably because he is constantly using it all the time, considering if the aforementioned statement is actually true).
It gets even more ridiculous in the sequels. Animal Talk is possible with the appliances all of a sudden starting with the second movie (there were animals in the first movie too, and none of them were able to talk to the appliances), and they really begin pushing the envelope by having sapient sinks and balloons in the third movie.
Beauty and the Beast actually did this with furniture. Considering the fact that all of the Beast's servants were turned into furniture due to a magic spell, it's actually never explained what happened to the actual furniture inside the Beast's castle.
The west wing of the castle has been more or less destroyed over the years by the Beast's various rampages. Now, was he simply vandalizing his own furniture, or...
In The Little Mermaid Max the dog and Glut the Shark act like a normal dog and shark respectively, whereas the other animal characters (like Flounder, Scuttle, and Sebastian) can talk, sing, and dance. Even Flotsam and Jetsam, Ursula's moray eels can talk.
Which leads to some Carnivore Confusion too; if all fish can talk, what the hell do mermaids eat? They can't eat sentient fish, because they consider that evil and a reason to hate humans but apparently non-sentient fish don't exist. Do all these merpeople subsist on seaweed?
In the series, a frequently mentioned merfolk dish is 'plankton pate'. So does that mean merfolk eat like whales?
In the 1940 short Mr. Mouse Takes a Trip,Pete mentions that he used to have a cat.
There's a bizarre inversion style case in one Donald Duck comic book story where anthropomorphic animals are acting so much as stand-ins for humans that they treat an anthropomorphic animal as an anomaly. The story revolves around a rat-man creature people have encountered in some sewers. Everyone treats this much like a werewolf (or -rat) among humans, not believing in it before they see it and then thinking it a monster. In the end, it turns out to be a Scooby-Doo Hoax cooked up by some cat criminals. So the terrifying anthropomorphic rat monster turns out to be a run-of-the-mill anthropomorphic cat person in a costume.