Most Funny Animal, Civilized Animal, or Talking Animal characters' surnames, if they have one, go with their species. These often come with the middle initial "T," which of course stands for "The," or "J," following an old cartoon tradition.) In some cases the species name is used as a surname, but seems to be just a descriptive term, with a definite article, as in "Edd the Duck" or "Kermit the Frog."
Bonus points for making it into an Alliterative Name.
Note that, considering surnames originally emerged to be descriptive ("Where's Todd?" "Which Todd? Andrew's son, Todd?" (Anderson) "No, Todd the blacksmith." (Smith) etc.), this is not all that ridiculous. Considering how inter-species marriages never seem to happen, (unless they're main characters) it seems likely that a Funny Animal will have a surname related to their species. Also the fact that all members of a species share a common ancestor.
When it's the species that takes a character's name, it's A Kind of One. When it's Dog Smith instead of Alice T. Dog, it's A Dog Named Dog. When it's not the actual species name but a pun on it, that's A Lizard Named Liz.
In the Ariadne Magic Academy we have Catgirls J. von Katze and S. du Chat (whose surnames are, respectively, German and French words for "cat").
Tony Tony Chopper of One Piece. "Tony" is a nickname based on "tonakai", the Japanese word for "reindeer".
Bucky OHare. And for bonus points, his one-eyed robot is named "Blinky."
Bamse. Has pretty much every variant used at some point. (Personal favorite is Unlucky Childhood Friend Vargen's ("The Wolf") object of affection, Virginia Wolf, literary reference and animal surname in one!
Pretty much everyone on Earth-C in Captain Carrot and His Amazing Zoo Crew! had a species surname of some sort—-or a species-related * first* name for some (see: Rubberduck's alter-ego of "Byrd Rentals").
Donald Duck comics show an extended Duck family, including: Gladstone Gander, Gus Goose, Molly Mallard, Cornelius Coot, Lulubelle Loon... you get the idea. Other friends of the family include Scrooge's secretary, miss Emily Quackfaster, or The Professor Ludwig Van Drake. Daisy Duck and Donald Duck aren't related, thankfully. And for bonus points: Donald's father was named... Quackmore.
Robert Crumb's Shuman the Human may have been named as a parody of this practice.
Lupo Alberto from the eponymous Italian comic character counts, because his name means "Alberto the wolf", but is also his legitimate name AND a pun on 60s actor Alberto Lupo; in the same comic there is also Enrico La Talpa, where "La Talpa" means "The Mole" (which is what he is), but is also his surname.
Also, the last name of the character Moses is implied to be Bobtail (a character called his father "Mr. Bobtail" on the phone), and he is, in fact, a bobtail dog.
Most of the characters from U.S. Acres, with the exception of Booker and Sheldon.
Calamity James' pet Lemming in The Beano is called Alexander Lemming.
A Polish children's magazine, "Miś", used to publish comics about a little Funny Animal bear going to school with other bears. Oddly enough, while his schoolfriends had normal human names, the protagonist himself had the name "Miś", "bear". Interestingly, "Miś" is also sometimes used in Polish as the diminutive of "Michael".
The Polish stop-motion children's series Miś Uszatek, about a kinergartener bear and his friends. Nearly everyone were named simply "Hare", "Piglet", etc. Lampshaded in one of the episodes, where Hare mentions that most other hares have more imaginative names (though they're all puns on something hare-related.)
In Piers Anthony's Xanth series, characters generally take their species classification as a surname such as Smash Ogre, Glory Goblin, Forrest Faun, Che Centaur, Tandy Nymph... On the occasional intrusion of Mundanes into Xanth, most characters are confounded by the existence of an actual last name. They usually just end up being called X Mundane for the duration.
It gets even better with mixed-species pairings: Glory Goblin married Harold Harpy and had two children: Gloha Goblin-Harpy and Harglo Harpy-Goblin. ....yes.
The Berenstain Bears children's books. Mama, Papa, Brother and Sister Bear. Brother Bear's original name was Small Bear, until Sister was born and his parents renamed him Brother. Every other character has a bear-related name. Too-Tall Grizzly, Lizzy Bruin, Mayor Honeypot, etc.
The first Redwall book featured this - John Churchmouse, Colin Vole - though since maybe three characters in total even had "surnames" they may not have been meant to be surnames so much as descriptions. The later books don't use species names as surnames, but species-specific names are common; hedgehogs are almost invariably something like "Spike" or "Stickle" or "Quill."
Johnathan Livingston Seagull (book and title character) as well as the parody Johnathan Seagull Chicken which uses characters with names like Segal and Fox as personifications of the corresponding animal
Another parody was Ludwig Von Wolfgang Vulture.
The children in The Lion, the Witch, and the Wardrobe make friends with Mr. and Mrs. Beaver. Mr. Beaver's best friend is apparently Badger. How this naming system works in a country populated largely by talking animals is never really explained, although it disappears later in the series; in the final book we have Jewel the Unicorn and Farsight the Eagle.
Both followed (Poink T. Ferret, Java Frog, Hump T. Camel, Hugh Manatee, Temp Ferret) and averted (Mutt Barker - illegitimate son of Bob, Arthur Bronswagger, Jimmy Noneck, Shak, Ezra Shawartz, Crappy Shawartz) on The Funday Pawpet Show. One of the newest characters, Cool Old Guy Gof, has a name that stands for Gray Old Fox.
In The Muppet Show, most Muppets of recognizable non-human species have one or another form of Species Surname.
Played with in an sketch on Sesame Street, where Kermit the Frog wanted a T-Shirt with his name on it, but the salesman kept mixing it up with shirts for Kermit the "Gorf," "Forg" and "Grof." Naturally, the other Kermits come in one by one for their own shirts.
Roland Rat, his brother Little Reggie Rat, and his friends Kevin the Gerbil, Errol the Hamster, Glenis the Guinea Pig, and Fergie the Ferret.
Kate Monster and Trekkie Monster in Avenue Q (though in this case "monster" is a race, not a species). Lampshaded when someone asks if they're related. They're not, and the exchange is the setup for a song called "Everyone's A Little Bit Racist."
Stretching the definition of "species" still further, one of the other puppet characters is named Lucy T. Slut.
Star Fox characters Peppy Hare and Slippy Toad. Also, Fox McCloud, Wolf O'Donnell, and Panther Caroso have their species as their first names.
Also Pigma Dengar, Leon Powalski (a chameLEON), Bill Grey, a greyhound, and Katt Monroe (cat with a K). Falco Lombardi would resemble a falcon if only he weren't bright blue. Whatever species he may be his name is clearly avian (he is the only bird in the series thus far).
But the famous Blue Falcon from F-Zero is also blue; the character's color may be a nod to this.
Sonic Chronicles gives Amy's full name as "Amy Rose the Hedgehog" (i.e., "Amy Rose" is a "double name," but her friends call her "Amy" for short), which makes her a straightforward example in that game.
In Pokémon Mystery Dungeon, the various Pokémon the player meets are all named simply by species. (One wonders what happens if two Bulbasaur ever show up in town.) The player, however, can rename his own character and any Pokémon that join his rescue team.
Lampshaded In the second game. A Teddiursa and Ursaring who were paired together couldn't tell each other apart when the former evolved.
Your partner is something of an odd case in the first two games, as they introduce themselves with whatever name you chose for them, which potentially makes them the only Pokemon in the world who has a proper name. Gates to Infinity avoids this by having your partner introduce themselves as their species initially, then having them ask you to give them a nickname later (Which they'll claim is the best name ever even if you didn't actually change it).
The Mario series has this, especially in the Yoshi's Island series, where the names were either a name or descriptive phrase in front of the species name (with the exception of Tap-Tap the Red Nose).
The Toads, natives of the Mushroom Kingdom, all share the last name "Toad."
Most mavericks in the Mega Man X series sport species surnames.
Satori Komeiji of Touhou uses her species as her first name as well: she is a satori, of course.
Done pretty cleverly in Sly Cooper, where most of the cast has a Meaningful Name of some sort or other. Carmelita Fox is, in fact, a vixen, but "Fox" is an actual surname, of course (for Hispanics, as well, such as Mexican President Vicente).
Also, unofficially or officially; Bentley Wiseturtle and Murry Hippo. As well as Raleigh The Frog and The Panda King,
Conker the Squirrel signs his name as "Conker T. Squirrel," which would make 'Squirrel' Conker's last name.
Stray animals in The Sims 3 are all named Stray Cat, Stray Dog, and Wild Horse. If adopted by a human family, particularly NPCs, their first name changes to a generic pet name drawn from a list, and their last name may or may not change to the same as the human who adopted them.
The sentient non-human races in Final Fantasy X use species surnames - Kimahri Ronso and Seymour Guado being the two most prominent (though Seymour is in fact half-human).
Kevin & Kell uses this trope widely. The main characters are the Dewclaw family, after a specific animal body part; there's a family of foxes with the surname 'Fennec', after a sort of fox with rabbit-like ears, and a local feline mechanic is named Aby Eyeshine (Abyssinian).
Used extensively in The Suburban Jungle - Starring Tiffany Tiger. An interesting variant used therein is Leona Lioness, who manages to work both species AND gender into her surname...
Rough Housing, the sequel comic currently in the works, has Charity Cheeger (Cheetah/Tiger hybrid), and Langley Lupina (wolf).
Grace Sciuridae in El Goonish Shive (Sciuridae being the formal term for the squirrel family). Extra points for her Code Name, Shade Tail, which is what the name actually means in Latin.
Eric Schwartz's Sabrina Online has a lot of fun with this trope. We have Thomas Wolfe, who is actually only half-wolf; his mother was a fox. He ends up marrying Amy Squirrel, who, not surprisingly, keeps her maiden name. There son ends up being one fourth fox, one fourth wolf, one half squirrel, with the name Timothy Wolf-Squirrel. Meanwhile, Fanon establishes Sabrina's surname as "Mephitidae" (the scientific family to which skunks belong to), while in the strip itself it's a "Where The Hell Is Springfield??" kinda thing.
And then there's Sheila Vixen. You have to feel sorry for her dad.
Played with a bit in Pv P Online by Skull the Troll. "Troll" is a straight example, but the "the" actually stands for "Theodore."
Subverted in Daisy Owl: Daisy isn't an owl, but her adoptive father is.
In Narbonic when Artie the hyperintelligent hamster is turned into a human, he takes on the pseudonym "Nick Cricetida".
Mell: Where did you get a name like Cricetida, anyway? Artie: It's my family name. Mell: Well, duh... Artie: Cricetidae. A family within the order Rodentia, comprising wood mice, voles, hamsters, and over 70 distinct species of gerbil. One Mongolian species, Meriones unguiculatus, is popular as a pet—
Poppy O'Possum. The title character is, as you'd probably guessed, an opossum. Though the artist has implied that she's adopted and the O'Possums are mostly a family of cats.
This is the case with all the dinosaur characters in The Tyrannosaur Chronicles. The main character, for example, is Traumador the Tyrannosaur. It is also implied that "the" is their middle name, with the notable exception of one of Traumador's friends, Norman a Centrosaur.
Tiny Toon Adventures uses this for a Running Gag; since Buster Bunny and Babs Bunny are the show's Official Couple, every time they introduce themselves together, they have to say, "No relation" afterward. This is eventually commented on in their cameo in an Animaniacs skit. (Noah: "Okay, let's hope not, this is a children's show...")
Several Walter Lantz characters, including Woody Woodpecker, and his regular opponent, Buzz Buzzard; and Andy Panda.
Camp Lazlo uses more than one of the name styles mentioned above; at least for those who actually have their last names mentioned (those of the three main characters aren't). Edward uses variation 1 (T. Platypus), Nina, variation 4 (Neckerly, which is alliterative), and some characters' names are exceptions to this: Clogmeyer for Samson, Smiles for Patsy and Lumpus for, well, Scoutmaster Lumpus (his full name is Algonquin C. Lumpus).
The premise of My Gym Partners A Monkey is that a clerical error turns human boy AdamLyon into Adam Lion, causing him to be sent to a school of animals (all of whom actually follow this trope).
Dinosaurs, the 1991 sitcom, revolved around the Sinclair family. Although the surname isn't a direct species reference, it is a reference to Sinclair Oil and its dinosaur logo.
In the Disney/Pixar film Cars, many of the characters have names reflective of the brand or style of automobile on which they are based: Mack is a Mack truck, Sally Carerra is a Porsche 911 Carerra, Lizzie is a Ford Model T "Tin Lizzie," Doc Hudson is a The Fabulous Hudson Hornet, etc.
A version of the first variation is found in The Animals of Farthing Wood. All of the original animals just have their species as their name: for example, "Fox," "Badger," "Toad" or "Weasel." Their descendants have differing names, though.
Several Transformers have names that reflect their alternate forms. Bumblebee, who later became Goldbug, turned into a yellow Volkswagen Beetle (bug) in both bodies. There's also Soundwave, who turns into a tape player; Cheetor, Rattrap, Waspinator and any number of others from Beast Wars, and Tankor and Jetstorm of Beast Machines, to name just a few.
In Transformers Animated it's shown that the name everyone goes by were assigned to them by their drill sargeant in Autobot boot camp, and in Beast Wars they apparently picked their own name upon discovering their new alt-forms.
An American Tail features Fievel Mousekewitz, Gussie Mausheimer, Tony Toponi (from the Italian topo, which means mouse). It also featured Warren T. Rat, although he was actually a cat in disguise.
Some of the first Droopy cartoons give his last name as Poodle. One cartoon gives him the name McPoodle.
Double time for Moose A. Moose, animated host of the children learning channel Noggin. In case you're wondering, yes he's a moose.
A fairly creative example can be seen in the civilian name of Darkwing Duck: Drake Mallard. The name has "hey, I'm a duck" written all over it, but they are also genuine names.
On the other hand, his sidekick is a McQuack.
It's also hard to tell where his daughter's name would fit in. She's apparently a duck (one episode cites she's got duck molecules, anyway), but her birth parents gave her the name Gosalyn, which sounds more like 'gosling' than anything duck related; she takes 'Mallard' as a last name after Darkwing adopts her.
Her birth surname is Waddlemeyer. That could reference either ducks or geese. Her birth parents are never pictured, but her grandfather, Professor Waddlemeyer, looks like an obese Ludwig von Drake, or a gray-haired Herb Muddlefoot; presumably a duck.
But when she adopts a secret identity now and then, the name she uses is Quiverwing Quack. Only ducks and pelicans quack, and Gosalyn is very definitely not a pelican.
Some of the rest of the cast follows this trope (Such as SHUSH agent Grizzlikoff) but most of them are too busy making other puns (like the scientist Sarah Bellum)
The Mighty Ducks had two of these: Mallory McMallard and Duke L'Orange. Say that latter one out loud. And then there was a character with the first name of Canard (the French for duck). Double bonus points for giving their all-too-human manager the surname Palmfeather.
Examples from Chip 'n Dale Rescue Rangers: Rat Capone and his sidekicks Sugar Ray Lizard and Arnold Mousenegger, Fat Cat's lackey Mole, Conrad Cockatoo, Mr. Starfish from Captain Fin's crew, Canina LaFur (from canine). It's highly unlikely, though, that Canina LaFur's evil stuntdog Zsa Zsa Labrador is a Lab Retriever.
Skunk Fu! uses species given names rather than surnames.
Jake the Dog, and in a bizarre occurrence, Finn the Human in Adventure Time. According to the creator, Finn is named "Finn the Human" because he is supposedly the Last of His Kind. Note that these aren't their surnames - they're brothers, as Finn was adopted by Jake's parents, so they'd probably have the same surname if it applied to Dogs in the Land of Ooo.
The princess-heavy show has some fun with this, in that there is even a character named Dr. Princess (it's her surname), who has no apparent connection to royalty.
Played with in The Nightmare Before Christmas, as while Jack Skellington sounds like a fancy use of this trope, there are some accents that pronounce "skeleton" as "skellington" (see Hot Fuzz for an example).
Technically, he could still be one, as only show-quality Manxes lack a tail. There also exist "stumpy" and "longy" Manxes, which have, respectively, partial or full tails.
In SpongeBob SquarePants, Mr. Krabs (Eugene H. Krabs) is a crab. Plankton also has this trope; "Plankton's Army" revealed that his full name is Sheldon J. Plankton. Patrick is a semi-example. He's a starfish (or, more properly, a sea star) and his name is "Patrick Star". Also, there's Squidward Quincy Tentacles, who's, well, a squid. Of course, SpongeBob himself probably counts too. (And he also wears square pants...)