Kou, Wakaba, and Aoba from Cross Game. A Running Joke that Aoba's many admirers get quite upset that Kou and Aoba are on a first name basis. Since they assume it means he's her boyfriend. Aoba is not amused.
Of course, this was after he called himself stupid under his breath and Rushuna initially called him "Mr Stupid", so he probably felt at the time it was more acceptable to be "Yatchan". Later on he seems to warm to the name.
Mirelle in Noir replacing "you" with "Kirika" after Kirika sacrifices finding out more about herself to save Mireille's life.
In Card Captor Sakura, Li Shaoran finally calls Kinomoto Sakura by her name, in both anime and manga, right after a near-death experience.
This was carried over in Tsubasa Reservoir Chronicle, where, when Sakura is the princess of Clow Country, Shaoran respectfully calls her 'princess' on every occasion, even though she insists that, as old childhood friends, they must stay on a first name basis. When Shaoran, later in the manga, exchanges Sakura's memories of him for the chance to save her life and politely addresses him as Syaoran-kun, he stops calling her 'Sakura' and reverts to 'princess.'
In the both anime and manga, after Li Shaoran calls her "Sakura", she asks if she can call him Shaoran. He stammers "do as you like" (his way of saying yes). This is also how Mei Ling picks up on their developing relationship when she revisits Japan later, noticing that they're on a First-Name Basis.
The scene in Tokyo Mew Mew where Aoyama Masaya first calls Momomiya Ichigo by her name instead of "Momomiya-san" is one of the unlucky ones to be passed over by the Englishtranslators, since the latter naturally always has characters use their first names.
Ichigo has a dream in which Aoyama asks her to call him by his first name, but still refers to him as "Aoyama-kun" until the end of the series.
In Episode 16, Retasu's first hint that the boy she has a crush on (with whom she is on a Last Name Basis) has already been taken is when the librarian calls him by his first name.
In Simoun, the fact that Angulas didn't say Aer's name at one point was a plot point... as, of course, was the moment when she did. And in the final episode, Yun happens to say Dominura's name Meanwhile, in the Future while thinking of her.
Occurs in both variants of Kannazuki no Miko where someone finds out that Himeko and Chikane are on a First-Name Basis, in both casis the third party is in no way happy about the prospect of a commoner calling the latter "Chikane-Chan".
Toyed with in Lucky Star. Konata finds that Kagami doesn't really have a nickname others can call her with (apart from occasionally "Kagamin"). In a fit of otaku-humor, Konata runs through several variants, until Kagami, in irritation, orders her to use "Kagami-sama" (very formal, respectful, and hinting at romantic feelings — Sylphiel's "Gourry dear" in the dub of Slayers was "Gourry-sama"). Konata does so, embarrassing her friend in the middle of lunch. They go back to the norm quickly.
Kagami also realizes at one point that she is on a first-name basis with people in Konata's class, and still on a last-name basis with people in her own class.
Yutaka has a bit of trouble calling her best friend Minami by her first name, even though her other friends have no problem doing so. She is finally able to after Minami addresses Yutaka by her first name.
During the beginning arc of Inuyasha, the title character initially refers to Kagome as some constant variation of the word "you", punctuating their strained relationship. After she helps him kill their first dangerous enemy, however, he switches to using her name. Kagome, who has absolutely no understanding for the art of subtlety, quickly points this out, much to Inuyasha's chagrin.
In Azumanga Daioh, during her fluffy dream sequence that includes Sakaki rescuing her from the other students on a white horse, Kaorin begs Sakaki to call her "Kaori" (which is her given name); unfortunately, she wakes up to her mother calling her by name.
Also, it is incredibly unusual for a Japanese teacher to be called by her given name. The fact that Yukari-sensei is never called "Tanizaki-sensei" by her students probably says more about the kind of person she is than any sort of change in relationship status, as we never see her being irritated by it or, alternatively, asking her students to do so.
Contrast her rival and old schoolmate Minamo, who is called "Kurosawa-sensei", as would be usual, until Tomo learns of her nickname of Nyamo and addresses her as Nyamo-chan. She is shocked.
Ayumu Kasuga somewhat feebly protests, but is forcibly nicknamed "Osaka" by Tomo, arguably indeed the kind of overly cheerful character who does such things. Soon enough everyone, even the class registry, only knows her as Osaka. Despite her initial vague concern, Osaka being Osaka, she pays it no mind shortly after being so nicknamed.
(Pre)Teen Genius Chiyo Mihama is always referred to as "Chiyo-chan".
Momoka in Keroro Gunsou is unable to call Fuyuki by his first name until she blurts it out while saving him from some alien cuisine that wasn't quite dead yet. Fuyuki, meanwhile, is oblivious to all of this.
Martian Successor Nadesico has Gai Daigoji, who insists on being called such instead of his real name Jiro Yamada which in Japan is considered a boring name, the equivalent of a name such as John Smith. Very few people, especially Ruri, call him Gai Daigoji, forcing him to continually remind people not to call him anything else. Gai is unfortunately shot in just the third episode of the series, probably to up the ante at an early stage and tell the audience that Anyone Can Die. People still call him just Jiro Yamada, but Akito Tenkawa who had become friends with Gai insists on calling him by his "soul-name".
First and foremost: Negi is never, ever addressed by any of his students by his last name! It's never "Springfield-sensei". His more polite students address him as "Negi-sensei", but many of them as "Negi-kun" or "Negi-bouzu".
Asuna's relationship with Negi parallels the honorifics she uses when referring to him. In the beginning, when she referred to him by name at all, it was never with an honorific (unless someone else was listening), a sign of how much she despised him. When she started to detest him less, she started referring to him as "-bouzu" (roughly, "kid"). Eventually, she comes full circle and starts using just his name again, as a sign of closeness.
It should be noted that, with Del Rey's tendency to keep honorifics and explain them, this translated into the English manga surprisingly well.
It should also be noted that other students also use this "honorific" as it is a pun. The Kanji for "Negi" can also mean "green onion" and "Bozu" can also mean "head" So in essence, they are cutesy-calling him "onion head."; a common term for children in Japan.
When Theodora, an actual princess note Third Princess of Hellas, is introduced to Negi, the most respectful honorific "-sama" is used. And she promptly tells Negi "You can call me Theo". Well, she's not Japanese. She should count herself lucky to get him down to "Theo-sama" before the episode is over.
Technically, Negi isn't Japanese either, he's Welsh. But he has referred to himself as an "English Gentleman," which no doubt annoyed certain Welsh readers... Of course, on an even more technical level, he's half Ostian, half whatever-Nagi-is. And on the royalty scale he probably outranks Theodora.
At the beginning of the series, Setsuna exclusively refers to Konoka as Ojousama, while Konoka calls Setsuna the much more informal and cutesy 'Secchan', admonishing her to refer to her as 'Kono-chan'. This represents the way Setsuna tries to keep her distance from Konoka, believing her to be above the simple peasant that Setsuna is, and their slowly growing friendship (and more) is demonstrated by Setsuna becoming increasingly willing to say 'Kono-chan'.
Near the end of the first Weiß Kreuz anime series, Aya conveys his gratitude to Tomoe Sakura for her efforts in protecting his sister by telling her his real name, Ran. Following this conversation, Sakura never sees Aya again, but his avoidance is for her own protection.
In Universal Century Mobile Suit Gundam, a lot of characters appear to be on first name basis, even when adressed as rank. Char Aznable was known to everybody as Char. Lt. Amuro instead of Lt. Rey. Captain Bright but never Captain Noa. In the English dub of Zeta Gundam, Kamille often addressed his favorite ladies by their first name followed by the honorific "Miss". For example, Miss Emma or Miss Recooa. Even bad guys went by their first name. Captain Basque, not Captain Om. Titans leader Jamitov Hymen was usually called Jamitov. The one exception is Paptimus Scirocco who was always called Scirocco by friend and foe. In some cases, inexplicably, the last name sounded more pronounceable and familiar with the first. Neverthless, Astonauge Mendoza was still usually called Astonauge. For obvious reasons, the Zabis all went by their first name so we could easily follow which was which.
In Mobile Suit Gundam SEED, following their official defection from the Earth Alliance military, Mu la Flaga significantly makes a point of calling Murrue Ramius "Murrue-san" instead of "Captain." The two of them lay the Will They or Won't They? to rest in the following episode and continue to call one another by name instead of by rank for the rest of the series.
Additionally, when Neo Roanoke recovers his memories during the finale of Gundam SEED Destiny and thus remembers that he is Mu La Flaga, he communicates his recovery to Murrue by calling her by her first name for the first time in the series.
More or less the entire crew does this to each other after leaving the Earth forces during Gundam Seed. Kira goes from calling the crew of AA from their rank and last name (Captain Ramius, Major La Flaga,Lt Badguriel) to their first sames (Murrue-san Mwu-san Natarle-san) leaving the san because they are a good 10 years older than him and he is very polite. That last one is odd since Not only is Natarle is already gone from the this point and is their enemy but Kira never speaks to her again in person anyway. There's big scene about this change though Kira just flys in to save them asking Murrue if she's alright using her first name without provocation and that's the way the crew acts from then til the end of Destiny. Oddly Andy Waldfeld is the only member who doesn't get this. He's always referred to as Commander Waldfeld by everyone. Murrue and Mwu are also on a first name basis with Athrun, which is kinda strange since Murrue has never spoken to him ever in both Seed and Destiny and Mwu only a handful of times.
Also happens with Kira who first uses a honorific when talking with Lacus Clyne who asks him to refer just by her first name. Ironically, Lacus also used a honorific to Kira the first time they talked.
This trope is very common in the Gundam franchise as a whole—Colonel Michaelnote Gern, Major Ulubenote Ishikawa, and Captain Grodeknote Ainoa are just a few examples. There are a few who use last names, but there's no explanation for the convention or exceptions to it.
Kyon calls Haruhi by her first name after the chronological sixth episode, which served as the series' climax in the original non-chronological episode order, since at that point their relationship becomes much more intimate, as reluctant as both are to admit it. Haruhi in turn of course, calls people exactly as she likes.
When Kyon addresses Haruhi familiarly in the alternate timeline, she's offended until he tells her that he's John Smith.
For some reason, Yuki never, ever calls Kyon anything but "anata". This is a minor plot point in one of the later short stories. This could be because he's apparently the only person she talks to.
Inversion: Mikuru asks Kyon to call her by her first name fairly early on, but Kyon continues to refer to her as "Asahina-san". He does this both out of respect and to try to prevent them from growing too close, as that would have some bad consequences...
A inverted version appears in Ranma ˝, in an episode where Ranma and Genma unknowingly go back in time to a point before Ranma and Akane first met. One of the first clues that something is wrong comes when Akane scolds Ranma for yobisute (calling her "Akane" with no honorifics).
At the end of Season 1 of Magical Girl Lyrical Nanoha, Nanoha tells Fate that that the first step to becoming friends is to call each other by their names, and for the first time in the series, Fate says the name "Nanoha".
Nanoha seems to prefer being addressed by her first name, since she has her subordinates call her Captain Nanoha rather than Captain Takamachi.
The manga of the third season has Subaru calling Teana by Tea when she noticed her partner finally calling her by her first name. Teana immediately denies anything changing in their relationship and states that she's only doing that to differentiate Subaru from her sister! Really!
In StrikerS Sound Stage X, Ginga suggests that Runessa refer to her by her first name so that she doesn't get confused as to whether she's referring to her, her sister Subaru or her father. Runessa does likewise, noting that her last name is fairly common.
For no explicitly given reason, Shamal goes from referring to Fate as "Testarossa-chan" in A's to calling her "Fate-chan" in StrikerS.
Well, she did get the surname "Harlaown" during the interim.
In Futari wa Pretty Cure, the switch from "Misumi-san" and "Yukishiro-san" to "Nagisa" and "Honoka" happened at the end of an episode focusing on the question of whether the characters in question were, in fact, friends.
Similarly, in Yes! Precure 5, after fighting for a whole episode, Rin and Karen used each others' first names as an indication of having developed respect for each other. For the most part, this stuck.
In Digimon Adventure 02, Daisuke switches calling his Fusion Dance partner from "Ichijouji" to "Ken." Ken, on his part, goes from "Motomiya-kun" to "Motomiya" to, finally, just "Daisuke."
Mai and Yuuichi begin on a Last Name Basis, but after Yuuichi is resurrected they call each other by their first names.
In the side novel, "Natsuki no Prelude," Shizuru, who is initially Natsuki's only friend and turns out to be in love with her, is noted as being the one person with "the gall to address Natsuki by her first name" before the start of the story.
Reito tends to be addressed by his first name by most people, and in Episode 7, asks Mai (whom he has a crush on) to do the same.
In Sailor Moon, the first time Helios/Pegasus calls Chibiusa by her name is when she finds him after he has been captured by Nehellenia, and Chibiusa comments on that. In the Cloverway dub, he had already called her "Rini" before, so they had to change the scene to have him call her "Minimoon" instead, which doesn't make sense because it's not her real name.
Smaller example: Everyone calls Haruna-sensei by her first name. The DiC dub switched it to make "Haruna" her last name (which is Sakurada in the original).
In the fifth episode of the live-action Pretty Guardian Sailor Moon, Ami tries to change herself (more extroverted) in order to be "a better friend"; she does things like cheerfully greeting the entire classroom when she enters, sitting with Usagi's friends at lunch, and going to a pajama party with Usagi and Naru. At the end of the episode, Ami realizes that she doesn't have to change herself to be a good friend, and so things revert to normal. When Ami doesn't join Usagi's friends at lunch, they begin discussing her as though she's an outsider again, and it seems as though this episode accomplished nothing as far as their relationship... however, the group has definitely started to think about Ami differently, as Usagi suddenly realizes:
Usagi (thinking): Naru-chan and the others, they're saying Ami-chan.
In CLANNAD, Tomoya and Nagisa originally referred to each other with their last names. Fuko tries to convince Tomoya and Nagisa to call each other 'Tomoya-kun' and 'Nagisa-chan'. Nagisa switches to 'Tomoya-kun' with some difficulty, but Tomoya finds he can't add the '-chan' at the end, and just refers to her as Nagisa from then on. Of course, when Fuko disappears, Tomoya finds himself wondering when and why he started calling Nagisa by her first name.
Kotomi only responds (at least at first) to Tomoya (or anyone for that matter) when called Kotomi-chan. Taken to ridiculous extremes when Sunohara visits the library.
Sunohara: I got- completely ignored. She won't react to small talk. It pissed me off, so I threw books everywhere and knocked bookshelves over, but she still ignored me.
Also a subtle plot point in Kyou's route in the Visual Novel. Tomoya refers to Kyou by her first name (by Kyou's request when they first met, to differentiate her and Ryou), and calls Ryou by her last name, Fujibayashi. She goes out of her way to try and get Tomoya to call her Ryou, which he does, somewhat... but it doesn't come naturally and they don't grow closer romantically. It IS Kyou's route after all.
In Gravitation when cold fish Yuki finally begins calling Shuichi by his first name it is a sign that their relationship is evolving favourably. Needless to say, Shuichi is overjoyed and does not lose the opportunity to comment on it, much to Yuki's chagrin.
In Koihime†Musou a lot of emphasis is placed on the fact that certain characters address each other by their private names, like between Chouhi and Kannu.
This comes up in Flame of Reccawhen in the last chapter Yanagi asks Recca to call her by her name instead of "hime".
Commented on in canon—Uryu gets upset when Ganju calls him by his first name. Most of his schoolmates refer to him as "Ishida-kun" or just "Ishida", indicative of his aloof personality. The only people who refer to Uryu by just his first name in the original Japanese are his grandfather and father (the latter of whom Uryu calls by his first name, which indicates a strained relationship even by Western standards). The English translation erases a layer of social complexity by having all the Karakura High characters call Uryu by his given name.
Hitsugaya and Byakuya take issue with Ichigo calling them by their given names, although in Toshiro's case, it is because of his desire to be called "Captain Hitsugaya" at all times.
At the end of the Soul Society Arc, an impatient Ichigo jumps into a hospital window and asks Kuchiki Byakuya and Renji if they've seen Rukia. After his departure, Byakuya wonders aloud if Ichigo is going to continue calling him by his first name.
Near the start of the manga, Ichigo worried people heard him screaming Rukia's first name on national TV. He was anxious of the rumours that would start in the She's Not My Girlfriend kind of way.
In the third movie, Renji, who has forgotten Ichigo due to the main villain's special ability, objects to being called by his first name.
In the Amagai filler arc, Amagai calls Izuru by his first name when he comes into the office, startling him and causing him to have a flashback of his old captain. He then says he was doing this to become closer to his squad, and then starts referring to Izuru by his last name from that point forth. Most other captains, with some exceptions, call their lieutenants by their first names.
The Visoreds all call each other by their first names even in the Past Arc, when some of them are captains and others are lieutenants.
Tsukishima appears to be the sole villain who calls Ichigo simply by his first name instead of his last name or the ever popular "KUROSAKI ICHIGO!".
In the UNMASKED databook, Orihime calls Ulquiorra "Ulquiorra-kun" in the comic short, much to his shock and and refusal. Although it is possible she didn't know his last name, it would be incredibly risky for her to act so familiar with him if they weren't already so, especially since "Ulquiorra-san" would have worked just fine. In the main story, she never refers to him by name; he tells her to only call her "Ulquiorra", possibly to keep some distance.
In One Piece, Robin initially called her crewmates by their titles on the ship to keep her distance, out of the fear that when the Marines pursuing her start closing in, they would betray her to save themselves. She sometimes made an exception for Luffy, who had agreed to take her in, although this is presumably on a professional basis, in the same way she would call Crocodile by his real name. After the Enies Lobby Arc, she begins calling them by name. Some of Luffy's crew members (Sanji, Chopper, Robin and Franky) typically start out calling him "Straw Hat", the nickname his enemies commonly use, but except for Franky, refer to him by name after joining.
At least in the anime, Franky has started calling Luffy by his name as of Episode 405. He also typically refers to Robin by her full name of "Nico Robin."
She still calls Zoro 'Mr. Swordsman/Mr. Bushido' as a nickname. His position in the crew is actually the swordsman. She does refer to him by his name at one point after the timeskip.
In Darker Than Black, Kirihara is chagrined when November 11 immediately starts calling her by her first name, Misaki, after they are introduced, and expresses her intention to call him Mr. Simon (he introduces himself as Jack Simon) In later episodes, when she has gotten to like him more, she doesn't object to him calling her Misaki and refers to him as November or November 11.
In Fruits Basket, after Haru apologizes to "Honda-san", Yuki says that he could just call her "Tohru".
The first time Tohru called Yuki "Yuki-kun" instead of "Souma-san," Yuki turned bright red, turned into a mouse, and fainted. Tohru continued to call him "Yuki-kun," though, but Yuki only called Tohru by her name at the very end of the manga.
Machi calls Yuki his name at the end after having only called him president-san
To an extent Yuki's acquired nickname of Yun-Yun which he tells them to stop using in case it stick or he gets used to it...they don't stop
Also, Kyou jumping straight to this from Hey, You! after the Cat's true form incident is probably the biggest early hint to his feelings for Tohru.
Inverted in Akikan!. Secretary Airin Kizaki does not like her boss, Hidehiko Otoya, to call her by her first name, always leading to this exchange.
Hidehiko: Airin-kun? Airin: It's Kizaki.
It's not just her boss, a few times Daichi does the same and she objects (they're both unrestrained perverts)
In Legend of Galactic Heroes, Reinhart and Fraulein Hildegarde von Mariendorf try to get on a first name basis after they had fallen in love, got engaged and with a child in the making Hilarity ensue when they silently decide to remain formal calling their spouse "Your Highness" or "Fraulein after a very awkward attempt.
Upon first meeting his best friend Siegfried Kircheis, at age ten, Reinhard outright rejected his first name as "too common," and thereafter always refers to him by his last name, Kircheis which he likes much more.
There is also the scene where Yang is trying to propose to the newly-promoted Frederica. He makes several false starts, addressing her as "Lieutenant," then "Major," then "Miss Greenhill", before finally using her name.
When Hildegarde pays a visit to Annerose she initially adresses the latter as "Countess Von Grünewald". When Annerose suggests switching to first name basis Hildegarde is happy to oblige, even telling Annerose to use the familiar form "Hilda".
Nishizawa, upon getting closer with Hinagiku in Hayate the Combat Butler, tells Hinagiku to call her "Ayumu." It's this act that causes Hinagiku to stop pursuing Hayate as a love interest and work behind the scenes to support Nishizawa's attempts.
To the point that she feels uncomfortable when she does realize her interest in him, and unnerved when Ayumu does the same thing to her.
When Hinagiku first met Hayate, Hinagiku uses 'Hayate-kun'. When he uses her weakness against her, she reverts to 'Ayasaki-kun'. After she realizes that she's fallen in love with him, she returns to the first.
Hayate and Hinagiku try to use Athena's first name to create a nickname. It works for Hayate, but it angers Athena when Hinagiku tries to do so, shocking her back to referring to her as 'Tennousu-san'.
Rather significant relationship point between Jinto and Lafiel in Crest of the Stars. Lafiel is the granddaughter of the Empress and Jinto is the only person other than her immediate family who uses her given name. This is because he didn't realise exactly who she was when they first met, and Lafiel was delighted to have someone around who treated her like a normal person. When he later learns the class differences between them, he tries to be formal, but it quickly becomes clear that she's hurt by this, so he starts using her name again. When they start serving together, he calls her Captain when on duty but still stays on a First-Name Basis off duty which raises a lot of eyebrows.
In a chapter of Fullmetal Alchemist, Riza claims the Colonel calls her by her first name when they're alone, but she's only trying to trick Envy into blowing his cover after he transforms into Roy.
The only person who Mustang is on First-Name Basis with in the series is Maes Hughes (and vice versa). Almost ironically, Mustang is one of the few characters who doesn't call Ed by his first name. The two Armstrong (Alex and Olivier) both, naturally, refer to each other by first name.
In Yu-Gi-Oh!, everyone calls Yugi by his first name, even though he most often calls them by their last names. Interestingly enough, characters may be on a Last Name Basis with one character and a First-Name Basis with a younger sibling they don't know as well, in order to distinguish the two (for example, the characters often call Seto Kaiba "Kaiba-kun" and his younger brother Mokuba "Mokuba-kun").
It's mostly because Mokuba is friendlier, and thus less likely to object, while Kaiba can often be outright hostile when the main characters talk to him.
Pretty much everyone calls Judai by his first name, except Sho and Kenzan who call him "Aniki" (Big Brother/Boss) instead.
Fubuki tells Manjoume three times in one episode to stop calling him "Onii-san" when he's still angry over Manjoume brainwashing his sister.
After Sho's A Day in the Limelight in season 3 (which has been a very traumatic season for everybody), he starts to call Judai by his given name instead of Aniki, to show how furious he is at Judai. After Judai fuses with Yubel and Sho realizes that he's forgiven Judai for what happened, he screams 'Aniki' after him, and afterward calls him 'Aniki' again, or Judai-aniki.
This trope is invoked by Manjoume, who insists that everyone call him "Manjoume-san"...except Asuka, who he has a severe crush on. She is the only person he's ever given permission to call him by his given name of "Jun" to. She still doesn't do it.
Everybody calls Yusei by his first name. Some other characters such as Crow are called by their first name all the time.
Yusei gets Aki's attention during their second duel (where she's having a psychic mental meltdown) by switching from "Izayoi" to "Aki." Jack is still the only one of the main cast who doesn't call her by her first name.
Rudger Goodwin is always referred by his first name to distinguish him from his younger brother Rex Goodwin, whom everybody calls by his last name instead.
Yu Gi Oh Zexal: Everyone calls Yuma, his pals or Kaito by their first name. Only a few characters actually call Shark by his given name instead by his nickname.
Yuya and Yuzu are called by their first name by everyonenote except by Nico Smiley if they are in the middle of an official match he is doing the Combat Commentary. However, Yuya and Reiji go with Full-Name Basis with each other.
Yuto is the only character who calls Kurosaki by his first name, since they are best friends. And since Kurosaki was introduced by his given name first, the majority of the fandom sticks with his given name, despite the constant Last Name Basis around him.
Similarly, in YuYu Hakusho, most of the main characters call Yusuke by his first name, and while everyone except Yukina and Shizuru call Kuwabara by his last name, most people call Shizuru "Shizuru-san." Interestingly enough, Kuwabara calls Keiko by her last name, Yukimura, in the manga, but calls her "Keiko-chan" in the anime.
During the penultimate battle of GunBuster, Noriko calls Kazumi by her first name to snap her out of a Heroic B.S.O.D.. Much explosions, attack calling, and physics-breaking ensue.
In Transformers Victory, it's a notable moment when Blacker refers to Wingwaver by name instead of calling him "kid". They don't get to respect each other for a couple of more episodes, however.
In Ga-Rei, it's worth paying attention to what everyone calls each other after Kagura loses her memory. Izumi calls Kagura either "Tsuchimiya-san" or "Kagura" depending on whether it's Yomi speaking or not. Kagura, who used to call Kensuke "Ken-chan", goes from calling him to "Nimura-kun" to "Kensuke-kun" as she gets to know him better. Again.
Everybody in Naruto seems to be on a First-Name Basis with each other. Even the polite characters like Hinata and Lee use first names with Honorifics that would normally demand last names. In fact, outside of the Hidden Leaf and Hidden Mist Villages, it seems like 99% of the cast has Only One Name to begin with (and it's worth noting that even some of the characters from the Leaf and Mist don't seem to have surnames either).
In flashbacks of Hashirama Senju and Madara Uchiha's childhood, it's revealed that shinobi during the warring clans era were instructed not to give out their surnames, in case they ran into someone from an opposing clan. Perhaps this practice ended up influencing present-day ninja culture by making First-Name Basis the customary form of address.
In Kizuna, the principal couple, Enouji Kei (extroverted, casual) and Samejima Ranmaru (introverted, formal), normally call each other "Enjouji" and "Ran-chan". When Enjouji's half-brother Sagano Kai first rescues Samejima from a drugging and rape attempt and then essentially rapes him himself, Samejima in confusion and anguish calls him "Kei." Told about it later by Sagano, Enjouji realizes how badly Samejima was affected because "He only calls me Kei when he really needs me by his side." Unfortunately, Central Park Media in their English translation flattened all of the names so that everyone uses the same ones and left out the honorifics, making this chapter in particular much less effective.
In Princess Lover!, Teppei is referred to as 'master' by the servants. Given his middle-class standard of living previously, this unnerves him and he asks for a less formal name, just using his name (first or last isn't indicated). Yuu refuses and they eventually decide on 'Teppei-sama', as she uses for the rest of the show.
A case in Detective Conan had a side plot in which Ayumi, realizing Ai Haibara was the only friend she called by her last name, tried to work up the nerve to start calling her by her first name. Haibara caught on by the arc's end and gave her permission, but shot down the boys when they asked if they could, too.
When Shinichi and Ran were children, there was a period of time in which Shinichi was more or less bullied into calling her by Last Name Basis, causing her to be confused (and somewhat heartbroken, given that she considered him a friend), but one epic adventure later they'd reconciled and were back on First Name Basis.
It's probably easier to name the major characters in the Pokémon anime that do have full names: Shigeru Okido/Gary Oak, Professor Yukinari Okido/Samuel Oak, Ash Ketchum, Tracy Sketchit, and Delia Ketchum. In fact, Ash and Tracey are the only main characters that have had a last name given and that is only in the English dub. Kasumi/Misty, Takeshi/Brock, Haruka/May, Masato/Max, Hikari/Dawn, Iris, and Dent/Cilan are only known on First-Name Basis.
Sousuke is a borderline aversion. He rarely calls anyone other than Kurz by their first name. In the first season, it took him quite a while until he got used to saying "Kaname" instead of "Miss Chidori". As for Tessa... despite her repeated requests, he only stopped using her rank in The Second Raid finale. It doesn't help she has a crush on him. As for the reverse, Kaname always called him by his first name but Tessa never stopped the Full-Name Basis.Which makes sense because Sousuke only knows the world of the miltary. Hence Kurz he can call by first name because they have known each other for a while and are roughly equal in rank.
Gauron calls *everybody* by their first name, including his victims. In Kaname's case, it's even worse — he calls her "Kana-chan" on several occasions — a diminutive form, that only her best friend Kyouko uses with her on a regular basis. And let's not even get into his pet names for poor Sousuke...
In Saiunkoku Monogatari, Shuurei is the only person who calls Ryuuki by his name instead of "Emperor" or "your highness", at his request. At one point she promises to always call him by his name when they aren't at some point of official function where they would get in trouble for it. Also comes up with Sa Sakujun, who Shuurei could never bring herself to call anything but "that man" or "young master".
Almost everyone from Neon Genesis Evangelion calls Shinji by his first name, but he's slightly more selective about the people he refers to by their first name:
In the TV version, he calls most of his friends by first name (Touji, Kensuke, Asuka...), but he never does the same with Rei except in the English dub (where he often switches off between her first and surname). He addresses most of the adults as "[first name]-san" (Ritsuko-san, Misato-san), except Kaji.
In the Rebuild continuity, he initially referred to Asuka as Shikinami-san until she asked him to use her first name while she chose to call him "Baka-Shinji".
Shinji and Kaworu reaches first name basis on their first meeting in the TV series, but in Rebuild it takes them until near the end of 3.0. In the manga, Shinji uses "Nagisa" until the end.
In School Days, Makoto and Sekai, who sits next to him in class, are on a first name basis, while he still calls his girlfriend Kotonoha by her last name, Katsura. Kotonoha's sister points this out as something unusual, and they move onto a first name basis after that.
The Girl Who Leapt Through Time — In a flashback of when Chiaki transfers into Makoto's class and the friendship between Makoto, Chiaki, and Kousuke develops, Kousuke lampshades it when Chiaki first calls Makoto by her first name. This is interesting because when Chiaki starts to date Yuri, he still calls her "Hayakawa-san," unlike Yuri, who calls Chiaki, "Chiaki-kun." He only calls Yuri, "Yuri-chan" once while talking about going to a nighters game with her to Makoto and Kousuke, though it was more to tease Makoto than really changing to first name basis. Makoto seems to be the only girl Chiaki is really informal with, though the reason as to why is quite obvious.
In Angel Beats! Kanade/Angel and Yuzuru Otonashi start calling by their names after they become friends and Otonashi got his memories back Otonashi is the one who starts that.
In Junsui Adolescence Nanao goes by a first name basis with her girlfriend Matsumoto, the School Nurse. In the beginning she is adamantly against it because she figures that Matsumoto doesn't feel the same way. Once they become a couple Matsumoto goes about happily calling Nanao by her first name in most situations without Nanao freaking out.
In Revolutionary Girl Utena, the vice principal and guidance counselor are having a talk with Utena when the chairman shows up. They're pretty shocked when Utena calls him "Akio" — they sweat bullets in his presence and prefer to call him "Mr. Chairmain, sir."
Happens occasionally in Katekyo Hitman Reborn! with changes of honorific, especially to show the change in relationships in the beginning of the Future Arc, but the most notable occur between Tsuna and Kyoko: first, at the end of the first episode, Kyoko asks to refer to Tsuna with the honorific '-kun' after he beats Mochida; second, TYL!Kyoko briefly refers to him by the pet name Tsu-kun, implying that they have become close in the future.
In Mai-Otome, most of the characters who used last names on each other in Mai-HiME now use first names, and use titles when formality is required. Arika tends to do so quite often, using first names on people such as the President of Airies and the Queen of Windbloom.
In the sound dramas, Mai starts off by calling Natsuki "Kruger-san," but after realizing that it's difficult to pronounce in Japanese, suggests "Kuga-san" instead, which Natsuki refuses. She then proposes First-Name Basis, which Natsuki accepts.
Referenced to in Pokémon: Diamond and Pearl Adventure! when Mitsumi says she and Cyrus aren't on a first name basis anymore. Incidentally basically everyone in the series is on a first name basis, as is Pokémon manner neither even have a known last name.
In Steins;Gate, whenever Okabe calls Kurisu by her real name instead of one of his myriad nicknames for her, it's a sign things are getting serious.
The thirteenth episode of Tiger & Bunny ends with Barnaby calling Kotetsu by his name for the first time. Kotetsu still calls him Bunny though.
Tomoe switched to First-Name Basis with Kotetsu after he rescued her from an warehouse fire — though not without a good deal of tsundere denial
Tomoe: That's right! So [the name "Tiger"] suits you perfectly, Kotetsu!
Kotetsu: Um, uh, did...did you just call me...?
Tomoe: Ah! Um! I-I-I just thought Kotetsu T. Kaburagi w-was too long, so I thought I would give you a little nickname!
Kotetsu: But Kotetsu's my real name...
Tomoe: I-it's not like it matters or anything!
Kotetsu: All right. Whatever you want, Tomoe.
Tomoe: I-I didn't say you could use my f-first name!
Kotetsu: [cough cough] Why'd you hit me? A-and right in the stomach...
Throughout Saki, Saki and Nodoka always call each other 'Miyanaga-san' and 'Haramura-san'. In the last episode, they finally agree to call each other by their first names (Saki-san and Nodoka-chan), complete with muchblushing, stammering, hand-holding, and pure, unadulterated Les Yay.
Hisa also starts off calling Saki "Miyanaga-san," but switches to calling her "Saki" by the time the tournament begins. She's also so far the only person who has referred to Mihoko by her first name.
In a flashback, Kana asks Mihoko to call her by her first name, and Mihoko complies. It has also revealed that she has started calling Hisa by her first name, instead of "Ueno-san"(her last name when they first met three years ago).
In the first episode of Boku wa Tomodachi ga Sukunai both Yozora Mikazuki and Sena Kashiwazaki get onto first-name terms (without honorifics) with Kodaka Hasegawa at their first meeting, much to Kodaka's surprise and amusement. Yozora and Sena never do the same with each other, unsurprisingly given their mutual hostility, and they don't seem to be on first-name terms with anyone else in the school.
In School Rumble Hanai and Mikoto are more on First-Name Basis with each other since they are childhood friends although they use honorifics in public for the sake of propriety. However during the survival game Hanai screams "Miko-chan!" when Mikoto gets shot. Its such an intimate nickname that it embarrasses the both of them to no end later.
In Kare Kano Arima and Yukino are having a romantic walk in Kyoto when the subject of going to a First-Name Basis crops up. They awkwardly and shyly try it out before a pair of their friends run past in a drive-by teasing.
In X1999, most characters are on first name basis with one another. One character, Sorata, is casual enough to be like that with everyone… except his love interest, who he politely refers to only as "neechan." Later on, they sleep together, and after he starts referring to her as "Arashi," no honorific.
Saori asks Miho if she can call her by her first name shortly after they meet. Miho takes longer to get onto a First-Name Basis with her friends.
In the "Little Army" prequel manga, Miho gets onto a first name basis with Hitomi and Chihiro in the first chapter. While Miho, Hitomi and Chihiro start calling Emi by her first name in the second chapter, she continues using their last names, until calling out Miho's first name as they're saying goodbye.
If Her Flag Breaks: When Nanami tells Souta her name, she tells him to refer to her by her first name, not her surname. She also warns him not to attach honorifics like "san or "chan" to her name.
In Anatolia Story, Yuri always refers to Kail as "Prince Kail" or "your highness". When they finally have a Relationship Upgrade, Kail asks her to drop the formality and refer to him simply as "Kail" when they're alone. For the rest of the series Yuri occasionally forgets herself and calls him "Kail" in public (usually hurriedly correcting herself), though no one bats an eye since by the point it's well-known that the two are deeply in love.
Played with in Yona of the Dawn. When Seiryuu started calling Yona by her first name and not "princess", the rest of the group asked if they could do the same, which she had no problem with. But Yona deliberately requested that her oldest friend Hak continue to refer to her as "princess" so she wouldn't forget that she was the daughter of a king.
Durarara!! is strange in that nearly all characters are called by their given name. The only character who regularly calls people by their surname is Anri. And even she says “Celty-san”, having only just met her.
The girls in School-Live! are all on a first name basis with each other, even with their teacher who they call "Megu-nee" instead of "Sakura-sensei".
Except on very special occasions, Kodocha's Sana and Akito never use honorifics when talking about each other, and always refer to each other as "you" and "Hayama" respectively.
In Love Hina, Keitaro always refers to Naru by the formal "Narusegawa" even after they're married, to which the rest of the cast then needs to point out that it isn't her name anymore, while she always calls him just "Keitaro". One exception is in one of his daydreams, where he fantasizes about marrying her. During the wedding ceremony he calls her "Narusegawa", then corrects himself to call her "Naru" — immediately freaking himself out at the implications of the more intimate form of address.
In spite of the gradual Slap-Slap-Kiss development of their relationship to the point of a mutual agreement to marry, Sango of Inuyasha continues to call Miroku "Houshi-sama" (referring to him by his status as a wandering Buddhist monk) instead of calling him by name, a distinction not carried over into the English dub of the anime. (The Latin American one resorted to "Excellency", referring to the authority given to Miroku as a monk.) Miroku, on the other hand, jumps directly to calling her "Sango" without honorifics almost as soon as they've met, although he attaches some kind of respectful honorific to the name of every other female he speaks to.
Kotomi from CLANNAD asks people straight away to add the suffix "-chan" to her name, probably in an attempt by the makers to show her child-like demeanor.
Nagisa doesn't have any problems when Kotomi calls her "Nagisa-chan" straight away either, which in this case points out her good-natured attitude.
In Nodame Cantabile, Chiaki starts out with calling Nodame various rude names, up to the point where they play the piano duet, when Chiaki finally calls Nodame by her preferred name.
Much later on in the series, Sai tries to learn about making friends by observing Naruto and Sakura, noting their lack of honorifics with each other, as well as the use of nicknames. This is somewhat subverted when he applies this knowledge, almost calling Choji "fatass" (Naruto saves his skin just in time). He then concludes that it is best to nickname a person the opposite of what he think they are, and proceeds to nickname Ino "Ms. Lovely." This earns him a smack from Sakura.
In Kamichu!, Matsuri demands from Yurie that they call each other by their first names right from the start, which is not all too respectful considering that Yurie is a god.
Immediate use of the First-Name Basis is very common for characters who are very (and we mean very) outgoing and friendly. Miyako of Hidamari Sketch does this when the circumstances of her and Yuno's first meeting are shown in the second series, almost straight away asking Yuno to call her "Miya" and running through a number of possible nicknames for Yuno until she settles on "Yunocchi". Then they have a bath together.
The same counts for Hikari's insistence to give Futaba a nickname in Amanchu!.
Even the fathers of Sia and Nerine have their different ways of addressing Rin. Forbesii calls him "Rin-chan," and Eustoma calls him "Rin-dono."
Not to mention their sensei calling him "Tsuchi," and Mayumi calling him "Tsuchimi-kun." Though these last two appear to be subversions of the trope at hand.
Hinagiku Katsura from Hayate the Combat Butler insists on being referred to by her first name by practically everyone straight off the bat (though with the "-san" suffix) — there's a teacher on campus who shares her family name and she doesn't like being confused with the teacher. Or to be reminded of said teacher. She conforms to normal standards when addressing others.
In Junjou Romantica, Nowaki addresses his long-time lover Hiroki Kamijo as "Hiro-san". After being together for some time, it starts to bother him that Hiroki's friends address him simply as "Hiroki", but when he tries it, Hiroki yells at him. After much angst and miscommunication, Hiroki reveals the reason why he prefers Nowaki to call him "Hiro-san": because Nowaki is actually the only person who calls him "Hiro-san". "I've got a special name I'm called, and there's only one person in the world allowed to call me that." Awwww.
Hiroko in AKB49 - Renai Kinshi Jourei demonstrated her strong friendship with "Minori" by insisting that "she" address her by her first name, not knowing that "she" is really her classmate Minoru, who still addresses her as Yoshinaga-san when not cross-dressed.
Given how formal Japanese society is about family and given names, this is a story point in Black★Rock Shooter. Yomi Takenashi is locked in a hospital room with her possessive childhood friend Kagari Izuriha, while Mato Kuroi is outside. Mato's voice causes Kagari to explode with rage. Lost in the moment, Mato calls Yomi by her first name. Yomi smiles (without realizing it) and Kagari turns on her. As Kagari gets more unstable, Yomi calls Mato by her first name while begging for help through the door.
Later in the series, Mato calls Yomi by her first name again, but apologizes. Yomi says it's alright though and returns the favor, indicating that they've become true friends.
In Bakemonogatari, Senjogahara gets Araragi to call her by her first name by bringing her father on their first date, and pretending that he's addressing her father when he says "Senjogahara". She doesn't reciprocate.
Averted with most of the Sohmas in Fruits Basket, since they all have the same last name. Tohru refers to most them by their first names, but adds "-san".
Also Played With between Arisa Uotani and Kureno Sohma. Kureno starts calling her "Arisa" once she gives her name, and she chews him out for being so "forward"; also, when she asks his name, he just says "Kureno", and she assumes it's his last name. Of course, Kureno's just a bit Socially Inept, since he never really interacted with people outside the family - he's so used to sharing a last name with everyone, he assumes that First-Name Basis is universal.