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.
(Sheldon) Plankton is referred as to plankton by everyone from SpongeBob SquarePants. even his own grandmother calls him Sheldon.
None of the kids (besides Butters) in South Park call (Eric) Cartman by his first name. Only the adults call him that.
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.
Futurama gives the page quote from an episode that introduces Fry and Leela's full names and lampshades this. Leela is introduced as Turanga Leelanote Turangalîlais the name of a symphony by Olivier Messiaen 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!?". note Leela's case turns out to be an aversion however after she meets her parents who are referred to as Turanga Morris and Turanga Munda, meaning Turanga is in fact her surname but she/the orphanage presumably never knew that.
(John) Zoidberg is almost never referred to by his first name. Mom and occasionally Farnsworth are the only exceptions.
An Fry is just simply refereed by his last name Fry to everyone
Mr. Burns from The Simpsons, 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!
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.
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.
Oddly enough, there were a few moments in Rugrats where Angelica would address Tommy as "Pickles," despite the fact that they are cousins and share the same last name.
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.
During the last season of Daria, Jane would occasionally call Daria by her last name, Morgendorffer. Usually, she was just teasing.
Howard Weinerman rarely calls (Randy) Cunningham by his first name.
On the villains side is (William) Viceroy.
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 brother, who is only ever called Wu.
Jimmy and Cindy from The Adventures of Jimmy Neutron 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.
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.
Miranda from As Told by Ginger is largely dismissive of Ginger and refers to her as "Foutley".
Shope is simply referred as by her last name shope from Supernoobs. Her first name is Jennifer.
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 for rest of the special.
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.
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.
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."