During the early part of their relationship, InuYashanever refers to Kagome by name, much to her annoyance. He starts addressing her by name after they team up to take on Yura.
Tyki Mikk from D.Gray-Man is pretty much always referring to his foe Allen as "boy".
Genma Saotome in Ranma ½ tends to call Ranma "Boy" (although not exclusively so), even/especially when Ranma is in girl form.
Nanjiroh Echizen also refers to his son Ryoma as "boy" sometimes in The Prince of Tennis. Additional, Momoshiro and Kaidoh call each other "Mamushi" and "moron", and Kamio also refers to Kaidoh as "mamushi". Until Kaidoh becomes the Seigaku captain in his third year; Momoshiro calls him by his surname, since he's implied to be his sub-captain.
In Digimon Savers, Piyomon calls Masaru just that, prompting a reaction of "Where's my honorific?"
Digimon Adventure 02: A jealous Daisuke calls Takeru 'omae', prompting Hikari to angrily reply, "It's not you, it's Takeru-kun."
The joke here, for those who don't know the nuances of Japanese language, is that Daisuke actually added the honorific "-kun" to the "omae" part. That's right, he just said "you" is Takeru's name.
The dub rendered this as "Hey, buddy!" for that particular line, and then continued the theme with Davis calling TK TO, TS, TA, etc.
In Cardcaptor Sakura, Syaoran calls Sakura anything but her name (usually preferring just "Hey You.", or "Kinomoto" if he really has to address her) He doesn't use her real name until the episode they're locked in an elevator together and Sakura falls through a mysterious hole. He's so shocked that he yells for her, calling her "Sakura," and when she floats back up by using the Float card, she acknowledges the change with happiness.
In the third Rebuild of Evangelion movie, the protagonist is rescued by someone he believes to be his long-term comerade and possibly love interest Ayanami Rei. After a while of failing to get any sort of recognition or reaction out of her and generally observing loads of disturbing empty-shell-like behavior from her, he finds out that "Ayanami Rei" was, in fact, the codename for a series of mass-producedartificialsoldiers, and that the " Ayanami Rei" he used to know died a long time ago, despite his fulite atempt to save her life. From that point on, he refuses to refer to the currently active clone by her name, reserving it for his fallen comerade. It leads to several situations where he refers to the current clone in roundabout manners such as "Why are we not alone?" to question the reason for her presence, or calling her "that other pilot.". Being told that she isn't who her programing tells her she is ends up throwing the current clone into a full-blown indentity crisis cumulating in a Heel-Face Turn of sorts.
Jun Manjoume of Yu-Gi-Oh! GX gets upset when people don't call him "Manjoume-san" and frequently retorts with, at first, "Manjoume-san, da!" and eventually simply "San, da!" Since "sandaa" is how the English word 'thunder' is pronounced in Japanese, he earns the nickname "Manjoume Thunder" at North Academy for this insistence.
One of the first hints that Kohane's home life isn't all that great is that her mother never calls her by her name.
In the first episode of Soul Eater, Soul twice refers to Maka with a term that has been translated as either "shorty" or "tiny-tits."
In Ikki Tousen, Hakufu usually refers to others by cutesy nicknames derived from their names: "Gaku-chan" for Gakushuu, "Mou-chan" for Ryomou, "Ryu-chan" for Ryuubi, "Fu-chin" for Ryoufu, "Ton-chan" for Kakouton, "U-chan" for Ukitsu, and so forth. The only ones she refers to by name are her adoptive sister Chuubou and her cousin Koukin.
Likewise, Kan'u is called "Kan-san" by the other two girls in her Power Trio, Ryuubi and Chouhi, whom she calls by their first names. (And of course, Hakufu calls her "Kan-chan")
In Hell Girl, Tsugumi calls her father "Hajime-chan".
Ban in Get Backers tends to address Ginji's friends with mean nicknames, such as monkey-trainer for Shido and thread-spool for Kazuki. (Although different translators use different names: ADV Films used "monkey boy" and "thread spinner", while Tokyopop uses "string-boy".) A flashback reveals that Ban originally had one of these for Ginji (lightning brat), before they got used to each other. Himiko mostly calls Ginji "you" (if she speaks to him at all) and thinks of him by his full name.
In Full Metal Panic!, Gauron tends to address certain people in an overly familiar way, and being the Jerkass he is, becomes even more persistent about calling them that way when they express discomfort and anger. Towards Sousuke, he insists on continuing to call him "Kashim" (and occasionally "Honey"), which Sousuke hates, because Gauron is not his friend. And then he called John Dunnigan by his first name "John," to which Dunnigan angrily told him to not do, since he only allows close friends to call him that. Gauron's response? Attack him, hold a gun to his privates, and threaten to shoot them off if he doesn't let him call him that.
In the novels he also calls Kaname "Kana-chan," something only her best friend Kyoko calls her.
He also addresses Kalinin in a very casual manner, calling him "Iwan (Ivan?)", a name no one else uses with him.
It should be noted that "Ivan" is not Kalinin's first name — which is Andrei. "Ivan" is more like an insulting way of addressing a Russian, and it's been widely used during the Cold War, at least in the European countries.
The original Japanese version of Dragon Ball Z features the Ginyu Force calling Vegeta "Vegeta-chan", which, of course, pisses him off.
In Magical Girl Lyrical Nanoha Strikers, Teana addresses Caro as "chibi-ko" (translated as "little one" or "kid") until learning her name. During the first season, Fate tends to refer to Nanoha as "you," or "that girl" until the Say My Name scene in the last episode.
In Ah! My Goddess, Keichi's and Megumi's parents require them to call them by names rather than "Mom" and "Dad".
In Bleach Ishida Uryuu calls his father by his given name. They are not on good terms.
Ishida doesn't like being called by his first name by most characters. Ichigo calls almost everyone by their first name, even Shinigami captains. (Some of them are very annoyed at this.)
Hellsing- Alucard purposely refuses to call his apprentice by her name Victoria Seras, resorting instead to a sneering alias "police girl" which shows his disdain for her reluctance to drink blood and embrace her vampire nature in full extent. On the other hand, when he does address her by name, shit has officially hit the fan.
Shizuo Heiwajima of Durarara!! is prone to this, either forgetting appropriate honorifics or forgetting names entirely, mostly because he doesn't really know any better. Tom notes that this is probably one of the reasons people would pick fights with him in school.
Takeru of Akuma de Sourou greets his crush's crush as Yuu-chan. Both Kayano and Kamijou are naturally horrified; this is not an introductory phrase. Of course, he wasn't feeling too friendly towards Kamijou, being his rival and all.
Van of GUN×SWORD is horrible with names, rarely even remembering the names of people he travels with for months. (He learns Wendy's name after a few episodes and one of the first clues that Priscilla is a love interest is the fact that he remembers her name right off the bat.) One the rare occasions when he does address people by name, he almost never uses honorifics.
Revolutionary Girl Utena: When Utena wins her first duel with Saionji, Anthy stops referring to Saionji as -sama and starts using -senpai to indicate she no longer has any obligation to be subservient to him.
In the beginning of Hatenkou Yuugi, Rahzel fights with Alzeid over this.
"My name is Rahzel! Not "hey you" or "stupid chick" or "little rat"! I'm not some kind of small animal!"
And when he finally does call her by her name, she gets upset because he didn't use an honorific like sama or dono. (Both are extremely formal and respectful.) She had to compromise on that, though.
Early on in Mai-HiME, Natsuki, not getting along with Mai, typically calls her just "omae", in contrast to referring to most of her classmates by last name without honorifics, and Shizuru by her first name. In Episosde 9, however, she starts calling Mai by her first name, as she starts to become friends with her.
Hibiki from Vandread always calls Dita "omee". The first and only time he calls her by name on-screen is the very end of the series finale, signaling a Relationship Upgrade.
Kyou from Fruits Basket usually addresses people as "you" or by a nickname or their first name. He doesn't bother with honorifics, contrasting with Tohru who always uses them.
Talking Bird Dela from Tamako Market addresses Tamako and other young female characters as "young girl", and Mochizou as "young man".
This was one of Robin's main (and yet subtle) characteristics in One Piece. It was very rare that Robin would actually say the name of the person she is talking to or referring to in any dialogue, preferring to use their designations (such as "Navigator-san" for Nami). This was her defense mechanism to protect herself and keep things impersonal to anyone she meets. After she finds her place with the Straw Hats, she begins to call them by their names.
The talking cat Sakamoto from Nichijou gets offended when he is called "Sakamoto" instead of "Sakamoto-san" by the Professor.
Yuki never refers to Kyon by name (either his real one or that nickname), instead preferring just "you."
Kyon himself uses the Japanese no-honorific variant. He addresses everyone except for Haruhi by their family names, but without any honorifics. His upperclassmen are the exception, but even then he's less polite than he should be. He calls them -san ("Miss"/"Mister"), when he should be using -sempai.
Invincible; William is very touchy about being called something shorter like "Will" or "Bill" to the point of absurdity.
Rick: I'm Rick Sheridan, can I call you Bill?
William: Only if I can call you "R-Sherry".
During the "Merged Hulk" period in The Incredible Hulk when the Hulk had Banner's psyche, he was a member of a group called "The Pantheon" whose other members were all related and were all named after Greek heroes. One (Paris I think) was an insufferable jerk who insisted on calling Doctor Robert Bruce Banner (who went by Hulk, Bruce, or Dr. Banner) "Bobby."
Slight subversion in Justice Societyof America: While evil, Todd referred to Alan as 'Father'; after becoming good again, he switched to the more casual 'Dad.'
In The Golden Age of Comic Books, comic character Johnny Thunder (who still exists, but a Re Tool or two has occurred) was connected to a genie-like "living thunderbolt". The word for summoning him was cei-u, but he never knew that, and was in fact unaware of the Thunderbolt's existence for a long time. Instead, he'd accidentally summon the Thunderbolt by yelling "Say, you!" at whatever bad guy he was confronting.
Played with in an issue of Suicide Squad, when Father Richard Craemer is appointed team chaplain:
Murph: So what do we call you? Father Richard? Reverend Craemer? Hey you?
Craemer: 'The Reverend Hey You' has a certain ring to it, don't you think?
In Lilly Epilogue Family Matters, Lilly's father refers to Hisao as "boy", and worse yet, always brings up Hanako's burn-related scarring when referring to her, even while she can hear him, which falls well into Kick the Dog. He does, however, start to call Hisao by his first name while acknowledging that Lilly is happy in Japan with him.
In The Power of the Mind one of Harry's employees, a rather shady guy named Steve, referred to everyone he knew as "Boss," "Sunshine" or for some reason "Dave."
In the US remake of The Ring, Rachel's son Aidan always calls her "Rachel", much to her annoyance. We don't know why this is exactly, but it becomes a plot point in the sequel.
"Hey you! Get your damn hands off—". George McFly in Back to the Future uses this at the dance because he expects Marty to be in the car. Instead it turns out to be the bully, Biff, so without backing down he rephrases his demand a little more respectfully as "No, Biff, you leave her alone."
In the Coraline movie, Coraline refuses to address her Other parents as Mother and Father, and after she realizes that the Other world isn't a dream come true, she deliberately calls her Other father "Hey you."
In The Pianist the Nazis address Jews by the familiar-form of "you": "du" (considered an insult in German when used towards strangers or new acquaintances). This is most notable in the scene where one Nazi is picking Jews out of a line to shoot: "du!...du!...du!". When the Good German, Capt. Hosenfeld, speaks to Szpilman he adresses him with the respectful formal "you": "Sie".
Albus Dumbledore likes to annoy Lord Voldemort by calling him by his first name, "Tom", which he hates. In the Final Battle of Deathly Hallows Harry follows Dumbledore's example, calling Voldemort "Riddle" (which is his real surname, the one of his Muggle father). The Dark Lord is not happy. Uncle Vernon also refers to Harry almost exclusively as "Boy".
The Marauders also bestowed the insulting nickname "Snivellus" upon Snape in their schooldays.
In the Discworld book Wintersmith, Granny Weatherwax names a kitten that was foisted onto her You.
Speaking of Pratchett: "It's an interesting fact that fewer than 17% of Real cats end their lives with the same name they started with. Much family effort goes into selecting one at the start ("She looks like a Winnifred to me"), and as the years roll by it suddenly finds itself being called Meepo or Ratbag."
Also also Pratchett: In Pyramids, we find that the name of the Discworld's greatest mathematician, who happens to be a camel, is "You Bastard".
Talking about "Hey you!", in Rincewind's experience, the time to start running is around the e in "Hey you!"
A Running Gag in Mort is that the other main characters all call Mort "boy", however many times he politely corrects them. By the end of the book, this has become a Berserk Button.
In To Kill a Mockingbird Scout always refers to her dad, Atticus, by his first name. So does her brother. They love him dearly, but they always call him Atticus. It's specifically mentioned that their mean old lady neighbor, Mrs. Dubose, is appalled by this and uses it as evidence that the whole family is degenerate. (They do also call him "sir," and at least once he insists on it when he's in a stern mood, but for whatever reason they've just always called him Atticus.) She also snaps at Scout for saying "hey" to her instead of "good afternoon." And in the same book we have Dill picking up on the fact that Mr. Gilmer keeps calling Tom Robinson "boy" during his cross-examination, and when Scout finally greets Boo Radley with "Hey, Boo," Atticus corrects her that it's "Mr. Arthur."
With three pairs of boots—but the worst of it was,
He had wholly forgotten his name.
He would answer to "Hi!" or to any loud cry,
Such as "Fry me!" or "Fritter my wig!"
To "What-you-may-call-um!" or "What-was-his-name!"
But especially "Thing-um-a-jig!"
Sideways Stories from Wayside School has two kids, Mac and Nancy, addressing each other with "You" and "Hey, you". As it turns out, though, they aren't being disrespectful; Nancy is embarrassed by his name and Mac by hers, so they never properly introduced themselves to each other. They still address each other this way, though, even when they start dating.
In Hungarian epic Toldi a general asks Toldi (the hero) on the field: "Hey, peasant! Which way leads to Buda?" Toldi is a noble and, as expected, takes offense at the general mistaking him for a commoner due to his clothing. He doesn't say a thing but answers by pointing to Buda with a long rake. One handed. The entire army goes "Holy shit, that guy's STRONG!"
In at least one of Robert A. Heinlein's books he bemoans the "degradation" of culture when a younger person can call an older one by their first name when they don't have an established friendship. According to him, this "lack of social politeness" is an indicator (or maybe a partial cause) of social collapse.
In the Star Trek: The Next Generation novel "Greater Than the Sum", Picard is interviewing officers for positions on his crew. One lieutenant (who's presented as a bit of a Bunny Ears Officer) introduces herself to the Captain as "Lieutenant Chen. My friends call me T'ressa. I've been known to answer to 'Hey you!'"
The title character of the Mediochre Q Seth Series was fortunate enough to know the current Prime Minister of Mantically-Aware Britain before she was famous, and can therefore get away with this more than most with her.
Queen MAB: "The line comes just after 'Kaz', Mediochre. I'd appreciate it if you didn't cross it again."
In The Mysterious Benedict Society series, the villain Ledroptha Curtain refers to Nichoalas Benedict's female assistant as "the woman" because he "refuses to refer to her by her ridiculous code name." Her code name is Number Two, which she prefers for everyone to call her, rather than her real name of Penicilla, which she doesn't like.
It's a turning point in Artemis Fowl and Holly's relationship when Holly finally calls Artemis by his first name instead of "Fowl" or "Mud boy" and much later, she calls him by an Affectionate Nickname "Arty". Similarly, when Artemis calls his mother "Mum" instead of the more formal "Mother".
In the Benjamin January series, set in New Orleans in the 1800s, the black protagonist repeatedly notes that white French-speakers, including children and strangers, address him with the familiar "tu", rather than the more formal and respectful "vous".
Live Action TV
On one episode of The Office, Meredith's juvenile delinquent son calls her by her first name. Dwight notices this, and after the boy is disrespectful to him too, gets a little revenge later.
Henry in Psych insists on being called by his first name.
Red and Eric have this dynamic in That '70s Show. Red calls Eric (and others) dumbass a lot of the time, Eric may call Red "Sir" to his face but usually calls him by his nickname but in a disrespectful way, not in a "equals" (à la Dharma and Greg) way behind his back.
Baby Sinclair on Dinosaurs won't call Earl anything other than "not the mama". Though he would sometimes actually call him "dada" or the like, when a situation asked for a Crowning Moment of Heartwarming.
In Square Pegs LaDonna (the cool group's Black Best Friend character) called the two leads "That Fat Girl" (Lauren) and "That Fat Girl's Friend" (Patty), even to their faces.
Scrubs has a bunch of these. (Dr. Turkleton, Marshmallow, Stick, Bobbo, girl names for JD...)
According to the Janitor, Lady (who was originally introduced by his shouting "Hey, Lady!" at her, which failed to convince JD they knew each other) has a brother named Him. Being the Janitor, of course, this may not be true.
In the episode "His Story IV", Doctor Kelso tells the collection of new interns that he can't be bothered to remember their names, so he'll call all the males Dave and all the females Debbie. One female says that's ok, as her name is Debbie, so he tells her that out of fairness to the others, he'll refer to her as Slagathor.
Have Gun — Will Travel features, as the main character, the mysterious Paladin, a gunslinger based out of old San Francisco who puts forth an image of refinement and education at odds with his violent profession. So, it's quite grating to the modern ear to hear him refer to the Chinese bellhop at his favorite hotel as "Hey, Boy"...especially since Hey Boy's real name was divulged in the show's first season! Still, Hey Boy seemed to embrace the odd moniker, going so far as to correct a stranger who once got his attention with "hey, you."
Kenan & Kel: Natural Born Kenan, when Kenan decides that he's adopted after finding no baby pictures of him nor any keepsakes of his childhood (they were destroyed in a basement flood), he starts referring to his parents, Roger and Sheryl, by their first names, thinking that they aren't his birth parents. After Sheryl requests that he stop doing this, he then refers to them as "Mr. and Mrs. Rockmore".
In the M*A*S*H episode "Potter's Retirement", Hawkeye addresses Colonel Potter as "Sherman" while trying to convince him not to retire his command. While Potter is depicted as a Regular Army officer who wouldn't ordinarily tolerate such familiarity like his predecessor, Henry Blake, would, in this instance he's clearly touched rather than angered by it.
In "Sons and Bowlers", Charles Winchester calls Hawkeye by his nickname during a rare bonding moment.
While all the M*A*S*H examples above are aversions of the trope, being clearly depicted as gestures of affection and respect, it's played absolutely straight with the other characters' habitually addressing FrankBurns by his first name, usually in a tone of voice suggesting a patient parent dealing with an especially dimwitted and recalcitrant child.
All in the Family: Archie Bunker insists on addressing his son-in-law Michael as "Meathead." The number of times he uses Michael's actual name can be counted on the fingers of one hand.
In the classic Star Trek episode "The Empath", Doctor McCoy decides to name an unnamed mute woman the crew encounters Gem, saying, "It's a lot better than 'Hey you'."
Star Trek: Enterprise: The two antagonists in the Temporal Cold War, Starfleet time agent Daniels and his Suliban opponent Silik, both call Captain Archer by his first name "John" (short for Jonathan) as a patronising way of indicating they know all about him. In fact, they even know things he hasn't done yet. Archer just ignores this provocation, usually because these two give him more serious problems to get angry about.
Captain Shran calls Captain Archer "pinkskin", which is generally a derogatory reference to humans.
Several Star Trek: The Next Generation characters have referred to Commander Data, an android, as 'it' in different contexts. Villains often use it as a pejorative, but it has also been used innocently by characters who simply don't realize that Data is a sentient being who should be treated as a person.
Notably, Dr. Pulaski insistently calling Data 'it,' or otherwise implying he was an object, cemented the fandom's dislike of the character. She was put on a shuttlecraft after season 2.
The Doctor (Emergency Medical Hologram) on Star Trek: Voyager apparently got this from time to time and once commented that "If I had a name, other than Doctor or 'Hey you', it might encourage the crew to treat me with a little more respect." He never did decide on a name, though in one alternate timeline, he became "Joe."
The Discovery Channel showed the recruitment process for the Green Berets called Two Weeks In Hell, and one of the recruits makes the mistake of referring to one of the drill sergeants as "Hey yo". The dressing down he received was surprisingly restrained.
Phil of the Future had an episode where Pim says 'Hey! You with the face!' as she tries to get there attention.
In 24's Day Five, President Logan has Special Agent Aaron Pierce tied up and demands that he keep silent about his role as the mastermind of the day's events or be killed. Pierce responds by calling Logan a traitor to his country and a disgrace to his office and that he vows to make him face justice, and caps it all by asking "Is there anything else...Charles?". Remember, this is a Secret Service Agent saying this to the President of the United States.
Queen's "Fight from the Inside" begins "Hey you boy! Hey you! Hey you boy! Think that you know what you're doing?"
Johnny Winter's "Hey You" consists entirely of the lines
Johnny Winter: Hey you!
Backup singers: Who, me?
Johnny Winter: Yeah, YOU!
Johnny Winter: ...oh, 'scuse me, I thought you were someone else.
Dream Theater's song "Vacant" begins with "Hey you. Hey you. I'm right here."
Comedian Brain Regan claims that he and may others will refer to people by some sort of nickname to get their attention.
Friend: My name's not "buckaroo"!
Brian: Su-sure it is..."partner".
If Garrus is with you at the conclusion of Mass Effect 1 and you decide to sacrifice the Council against his wishes, he will angrily refer to you as "human." This is particularly jarring since throughout the many conversions you have with him, he always politely and respectfully calls you either "Shepard" or "Commander."
In the third game, Javik tends to refer to most of the fellow party members by their species. Liara, particularly emotional after the fall of Thessia, angrily reacts to being called "asari" by saying "I have a name. It's Liara T'Soni, and I'd appreciate you using it from now on!" For his part Javik does use her name, though only to appease her.
In Disgaea: Hour of Darkness, Laharl refuses to call Flonne by her name (officially dubbing her "Love Freak", or settling with just calling her "you") until a particular plot point about two-thirds into the game.
Also, Laharl changes Dark Adonis Vyers, the very first boss of the game, into "Mid-boss". The name sticks.
Honestly, this trope is present in all Disgaea games. Characters rarely seem to address eachother by name on a a regular basis. In the third, we have "Fake Hero" Almaz, "That Delinquent" Raspberyl, and "The Princess" Sapphire as Mao calls them and they seem to address eachother as. And in the fourth, everybody seems to have nicknames for everybody. "Mr. Vampire/Weirdo", "Lass", "Whelp/Rascal", "Thief Angel", "Warden", etc. Disgaea seems to make it a point to showcase whenever characters acknowledge eachother by name as being significant.
In a skit from Tales of Symphonia, as he is giving out nicknames Zelos literally dubs Lloyd "Hey You" and Genis "Brat", while giving more affectionate nicknames to the female members.
Godot, the main prosecutor in the third Ace Attorney game, constantly calls Phoenix "Mr. Trite" to annoy him. At the end of the last case, however, Phoenix finally gains his respect and Godot addresses him by his proper name.
In Final Fantasy X, the protagonist - default Tidus - can be named at the start of the game, as is tradition in the series. However, FFX was the first game to feature voice acting, and as the protagonist could potentially be named anything, the characters in the game would only ever call him by pronouns. This is made worse in that not even Yuna, the love interest, ever utters his name - or even asks for it! The trope is carried over to the sequel where, even then, Tidus will only be referred to as 'You' or 'Him'. Final Fantasy XII fixed this by giving the cast set names.
Also, Tidus calls his father "Jecht" and "Old man," even to his face, to show his disdain.
Dissidia makes this part of the plot, with Tidus referring to/addressing Jecht as 'Old Man' for most of the storyline, but finally calling him 'Dad' after the dramatic fight that gets Tidus his crystal.
One of the earliest missions in Mechwarrior: Mercenaries is a training mission, where you take orders from a veteran mech pilot, who refers to you by the callsign 'Kid' or 'Hey You'. It's even in the mission description.
In Tales of the Abyss, Luke constantly refers to Mieu as "Thing." This turns into an (unintended) Insult Backfire when Luke later (after a lot of Character Development) tries to apologize to Mieu for the unflattering name, only to reveal that Mieu is proud that his beloved master gave him a name and doesn't want to lose it.
While Jet Set Radio has voice acting, none of the dialogue is fully voiced (except for Professor K and the villains). Instead, a short sound bite plays to indicate who's speaking. Whenever Gum (one of the GG's, the protagonists) speaks, she says, "Hey, you!". This also happens in the half-sequel/half-remake/half-Alternate ContinuityJet Set Radio Future.
There's a character in the webcomic Scary Go Round whose name is The Boy because the creator couldn't be bothered to give him a real name.
The Boy in Scary Go Round has a real name: Eustace. It's mispronounced "Useless" by Elodie, the French girl with whom he goes to stay, so he might be better off as The Boy.
Elodie was the one who GAVE him the nickname by accident in fact, refering to him as "le garcon" ("the boy") in some provided backstory when she first visited on an exchange.
Until very recently, The Boy's parents didn't have names either. They even referred to each other as "The Mother" and "The Father."
None of the three central human characters in How to Make a Sprite Comic in 8 Easy Bits have names - they're just "the author," "the friend," and "the girl."
The main character in Experimental Comic Kotonehas no name has a name that cannot be known by the reader. Kotone, of course, calls him Onii-chan, and Konstantine also refers to him as "My Brother" even though they aren't related. The others usually just use second-person pronouns. Occasionally, a speech bubble in which he would be introduced is obscured by something else.
This occurs in Cuanta Vida, where the BLU Scout refuses to address the BLU Spy nothing but gay slurs: "Cockfag", "Ass-monkey", and the memorable "Pickle thief", etc. Even after he confesses his feelings towards the Spy.
This occurs repeatedly in Homestuck, The Exiles always refer to the players as "Boy" or "Girl".
Shelley in South Park hasn't called Stan by his given name since Season One, generally preferring "Turd" or, on special occasions, "Stupid Turd."
Timmy's parents in The Fairly Oddparents do not have names of their own, being called only "Timmy's Mom" or "Timmy's Dad" when "The Turners" doesn't suffice. One time when Timmy went back in the past, his parents' real names were unrevealed using a Sound Effect Bleep.
In The Simpsons, Bart often calls his father "Homer" instead of "Dad". Probably a sign of how bratty Bart is, although Homer also usually refers to Bart as "the boy". It's actually a Running Gag that Homer is forever trying to get Bart to call him "Daddy," which never happens. (In one of the comics, an imposter is standing in for Bart, and Bart tells the impostor to remember to always say "Homer" instead of "Daddy".) The episode that flashbacked to Lisa's first word did a lot of jokes on it, too. One side effect is that, on the very rare occasion that Bart does call him Dad, it's usually very touching.
When The Simpsons was first airing, Bart addressing Homer by his first name was a bit controversial. Not only that, but there were a couple or so times that Bart made fun of his name, calling him "Homeboy".
Bart does call Homer "dad" as often as Homer though. He usually uses "dad" when talking about him to others and "Homer" when directly addressing him, implying Bart does this mostly just to annoy Homer, rather than being genuinely disdainful of him.
On Futurama, the will of Bender's uncle Vladimir includes his "loyal butler, 'You There', for his decades of dedicated service..."
Speaking of Futurama, Bender frequently refers to his organic coworkers as "meatbag(s)". Likewise, Dr. Zoidberg is almost never referred to by his title (granted, he's not much of a doctor), and Zoidberg also only refers to Bender as "robot" (or, more accurately, "rohbuht").
Stewie of Family Guy almost never calls his parents mom and dad. Most of the time he refers to Peter as "Fat Man" and Lois by her Given name. He also used to call Brian "the dog" (and addressing him directly as "Dog"), which seems normal enough for a dog except that Brian is human enough that nobody else does it (eventually he stopped doing this when they became more friendly to one another). In the earlier episodes, he often called Lois "vile woman". When his future self did call them "mom and dad", he immediately and violently corrects himself—"It's Lois and the fat man!"
An oddly affectionate version of this shows up in W.I.T.C.H., when Eric first acknowledges Hay Lin, he says "hey you" to her, she corrects him: "It's Hay Lin...". The next instance appears after Hay Lin saves Eric's life in "T is for Trauma": "Hey you, when did you get braces?" He continues occasionally addressing her with "hey you" for the rest of the series, Hay Lin doesn't seem to mind.
Cotton Hill only calls Peggy "Hank's Wife", even on the extremely rare occasions he wasn't being cruel to her on King of the Hill.
Helga's father, "Big Bob" Pataki from Hey Arnold!, usually referred to her "the girl", as she's the less-liked sister of perfect Olga. He also persistently called her "Olga," much to her annoyance.
Pete says this in a few classic Disney Cartoons such as 'Moving Day' and 'Mr. Mouse Takes a Trip'.
On Men In Black, Kay always calls Jay "Slick" or some other mildly disrespectful nickname, as a sign that he doesn't think Jay's skills are quite as good as he [Jay] thinks. In one episode, when Jay manages to untangle an alien conspiracy/plot by himself, Kay actually does refer to him as "Jay." By the end of the episode, however, he reverts to using "Slick," out of disrespect for Jay's golf swing.
"Slick" is also a genuinely affectionate nickname for Jay as well.
In another episode, following a major slip-up on Jay's part, Kay starts calling his partner "Sparky", telling him he has to work his way back up to "Slick."
In The Flight of Dragons, the characters challenge an ogre, and, not knowing its real name, resort to calling it "Hey, you!". When one of the party steps in to assist with the fight, we get this challenge:
Smrgol: "Hey, hey you!"
In Holly Hobbie And Friends, the title character and her friends named themselves as the Hey Girls after being addressed in this manner.
In the Buttons and Mindy shorts in Animaniacs, Mindy calls her parents "Lady" and "Mr. Man". Though at the end of Wakko's Wish, she finally calls her "Mom".
Sofia the First: Before Sofia felt comfortable enough to call her stepfather "Dad", he allowed her to call him "Roland" or "Hey you with the crown".
On House of Mouse, Mrs. Turtle would address Donald by shouting "HEY, DUCK!", though in one House story arc, she addressed Mickey by shouting "HEY, MOUSE!"
Children sometimes revert to this trope when trying to grab the attention of a friend's parents, especially with regard to mothers, who may or may not share a last name with their child.
Children may also use their parent's first name when there are a lot of parents around, because then "Mom!" doesn't help.
Or, an inversion: Some kids will use "Hey, Mom!" on a friend's parent, in an attempt to induce a double-take and get noticed that way.
Consider dating: at which point do you stop calling your girlfriend/boyfriend's parents "Mr. & Mrs. X" and start calling them by something less formal, be it "mom/dad" or their first name.
Can also be done between couples and good friends - referring to them as "you" can be a sign of affection, particularly in response to friendly mocking or teasing.
Spanish has two singular second person pronouns, "tu" (informal) and "usted" (formal). People with more authority than oneself are normally addressed formally, but even if a more fraternal relationship develops, the former underling may still be calling the other "usted." Argentinian Spanish replaces the "tu" with "vos".
French [tu v. vous] being closely related to Spanish has a similar system.
Many Indo-European languages have similar systems, it's just that many are falling out of use or are already considered archaic. In Irish for example, sibh would be a traditional way in some areas to refer to a priest but for everyone else, it would simply be tú. English went in the opposite direction and discarded "thou" which was once the informal way of talking in favour of "you" [related to French "vous"]. More detail can be found on the Other Wiki
Norwegian [du v. De] once had a similar system, but today, "De" has more or less disappeared in both spoken and written language. Addressing someone as "De" will often lead to the person noticing and either enjoying the extra respect or just thinking you're weird using a pretty much archaic polite form.