Jimmy and Cindy from The Adventures Of Jimmy Neutron Boygenius usually call each other by their last names as a sign of their rivalry. Come the episode "Stranded" Cindy calls Jimmy by his first name as the two get closer, surprising Jimmy and later Carl, Sheen, and Libby. To the point where Jimmy mentions that he wasn't even aware that Cindy knew his first name.
In Adventure Time, every single character (sans Marceline) calls Princess Bonnibel Bubblegum by her last name, Bubblegum.
From Ben 10, Dr. (Aloysius James) Animo is only addressed by his last name amino and even himself only uses his first name occasionally.
In Ben 10: Omniverse, Rook Blonko is addressed this way, but that's because his name is introduced with the surname first. Seeing as he is sent to Bellwood in America, and his species doesn't seem to leave their planet often, it could have been a mistake on Ben and everyone's part, thinking they were calling him by his first name.
Ulrich, Jeremie, and Odd of Code Lyoko are this way in "X.A.N.A. Awakens". It's implied Ulrich and Jeremie are this way due to their different social classes at Kadic though no explanation is given for Odd falling victim to it.
Danger Mouse has the title character's partner/sidekick, (Ernest) Penfold.
Baron Silas Greenback is commonly referred to as simply "Baron Greenback", or just "Greenback", as is seemingly tradition for villains who have more than just one name.
During the last season of Daria, Jane would occasionally call Daria by her last name, Morgendorffer. Usually, she was just teasing.
In Doug, Roger mostly addresses to Doug by his last name, "Funnie."
Captain (Leslie) Hero of Drawn Together. Through the entire run of the series, the only person who addresses Hero by his first name is his mother.
Duckman: (Eric Tiberius) Duckman, (Willibald Feivel) Cornfed, and (George Herbert Walker) King Chicken, although eventually their full names are revealed. Duckman is ashamed of his, and makes fun of Cornfed's name the first time it comes up.
Lois calls him Glenn and a number of other people as well, including his sister. It's mostly his drinking buddies who call him Quagmire.
Most of the Safety Patrol on Fillmore! refer to each other by last names, despite being middle schoolers. (Though if your first name was Cornelius, wouldn't you want to go by Fillmore?) Ingrid is usually called by her first name, but not always.
The page quote from an episode that introduces Fry and Leela's full names and lampshades this. Leela is introduced as Turanga Leela on the news, and a surprised Fry says, "Turanga!?". Amy points out it's her first name and calls him Philip while she's at it, and Bender reacts in the exact same fashion with "Philip!?". Although it eventually turns out that "Turanga" is actually her surname (her parents being Turanga Morris and Turanga Munda), but she/the orphanage presumably never knew that.
(John) Zoidberg is almost never referred to by his first name, but is known simply by his surname Zoidberg. Even he calls himself "Zoidberg". Mom, and occasionally Farnsworth, are the only exceptions to call him John.
(Philip J.) Fry is referred to almost exclusively by his last name Fry. Only his parents and brother call him Philip or Phil.
On Goldie & Bear, Bear's real first name is actually Jack. Bear is his last name. When he was little, he came to be known as "Baby Bear" and eventually the name stuck as just "Bear."
Jimmy Two-Shoes: The eponymous character is usually referred to as "Two-Shoes" by Lucius.
Her employer Dr. Drakken (real name Drew Theodore P. Lipsky) is usually addressed or referred to simply as Drakken. The same applies for one of the other villains, (Duff) Killigan, and for Kim's teacher (Steve) Barkin.
Also, Mr. Barkin addresses students by their last names; it seems to be a mix of formality and gruffness.
King of the HillHe's Known simply by his surname Boomhauer. It took 13 seasons for (Jeff) Boomhauer's first name to be revealed.
"Once-ler" is implied to be a surname in The Lorax 70s special.
(William) Murderface and (Charles Foster) Ofdensen in Metalocalypse.
In Monster Allergy, everyone, even his parents, addresses (Ezekiel) Zick by his last name Zick.
In The Mr. Men Show, various characters (usually Mr. Grumpy) sometimes refer to a Mr. Man or Little Miss without saying "Mr." or "Miss."
Coco Pommel from My Little Pony: Friendship Is Magic is one of the very few ponies described this way. She's usually called "Miss Pommel" aside from pre-season 6 episodes. This is due to a legal issue involving using Coco Chanel's name.
Garmadon from Ninjago is only ever referred to by a title, then his last name. Lord Garmadon when he was evil and trying to take over the world, and later Sensei Garmadon. He has a son named Lloyd Garmadon and a brother, who is only ever called Wu.
Howard Weinerman rarely calls (Randy) Cunningham by his first name.
On the villains side is (William) Viceroy.
The names of the Color Kids from Rainbow Brite are treated as their full names. Shy Violet is usually referred to as "Violet".note On the other hand, since "Violet" is also a common girls' name, "Shy" could just as easily be an adjective instead, making her a possible subversion of this trope.
Mr. Peterson from Ready Jet Go! refers to everyone by their last names. And yes, this includes his own son, Mitchell Peterson.
Mr. Burns, in that his first name (Charles) is hardly ever used. When people wish to refer to him informally, he goes by his middle name, Monty (short for Montgomery).
Smithers is also rarely referred to by his first name, Waylon.
Homer calls Ned Flanders by his last name. Justified in a Flashback when Ned introduces himself to Homer the day the latter moves into the neighbourhood, and having immediately rubbed him the wrong way by being himself, says
Flanders: Hi-diddly-hey, new neighbour-ino. My name's Flanders, but my friends call me Ned! Homer:Hello, Flanders.
Almost none of the kids (besides Butters) in South Park call (Eric) Cartman by his first name. Only the adults call him that. Kyle calls him "Eric" in the pilot episode. ("Come on, Eric, we're gonna go play at the bus stop!") Wendy, Kenny and Butters sometime called him "Eric". As a rule, fewer characters do as time goes on; by now, it's mostly just the adults.
(Sheldon) Plankton is referred as to Plankton by everyone from SpongeBob SquarePants. Even his own grandmother calls him Plankton.
Star vs. the Forces of Evil has Star's best friend from Mewni, Flying Princess Pony Head. Her real name is Lilacia, but everyone just calls her "Pony Head".
Agent Kallus' first name (Alexsandr) is only known thanks to Word of God from Dave Filoni, as it is not mentioned anywhere in either the show proper or the credits, even after his HeelFace Turn and defection from the Empire.
The commander of Titan Maximum is simply called Palmer. Even his grandparents call him palmer that, while his far-less-cool little brother is just Willie.
Initially played straight in the ABC Saturday Superstar movie Yogi's Ark Lark with Smitty, the Jellystone Park maintenance man, until he reveals that his first name is Noahnote Get it?..., after which, he is referred to by his first name Noah for rest of the special.