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 from Spongebob Squarepants. Not 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.
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.
Don't forget (Turanga) Leela, although it's implied "Turanga" is her surname. (In another episode, her parents are referred to as Turanga Morris and Turanga Munda, further implying that mutants arrange their names surname first - though Leela was not aware she was a mutant, it seems she may still have arranged the name that way.)
In one of the movies, the mailbox outside of Leela's parents house reads "Turanga".
This is lampshaded in the episode that introduced their full names, as seen in the page quote.
Lois calls him Glen and a number of other people as well, including his sister. It's mostly his drinking buddies who call him Quagmire.
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.
Given how Mr Burns was adopted by an eccentric old billionaire as a child, is its possible he was named after the Roman convention where Charles would be his pre-nom and Montgomery is his actual name (for example, Gaius Julius Casaer). Given how old-fashioned, eccentric and high-society he is, this would make a lot of sense.
Except Roman names don't work like that. Julius is Caesar's family name, and Caesar roughly corresponds to a nickname. It seems more likely he has a European style name, in which there is no "middle name" but rather a series of given names, one of which is the basis of the personal name.
Smithers is also rarely referred to by his first name, Waylon.
Her employer Dr. Drakken 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 called Palmer. Even his grandparents call him 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.
