Examples of Last Name Basis in anime and manga.
It is worth noting that family names come before given names in Japanese, Chinese and Korean usage.
Rurouni Kenshin has several characters referred to only by their surname, namely Shishio, Saitou, and Hiko. Misao is one of the few to usually address Kenshin by his surname "Himura".
In Blue Seed, Yoshiki Yaegashi, Daitetsu Kunikida, and Azusa Matsudaira are all referred to by their last names. While in the original Japanese dialogue their first names are never invoked, the English dub interestingly used their first names as a tool to denote a new level of intimacy regarding the romantic relationships of those three characters. Thus in the English dub Matsudaira is called "Azusa" by her ex-husband, Yaegashi is called "Yoshiki" by Koume when they start a relationship at the end of the series and again when they get engaged in the OVA, and Kunikida is called "Diatetsu" by Ryoko when they begin dating as well.
In Full Metal Panic, Sousuke calls everyone by their last names, mostly because of military discipline, and has actually had to be ordered to use first names.
And Gendo, when people aren't calling him "Commander" (or "Father"). Likewise Fuyutsuki. And does anyone know any of the bridge crew's first names except Maya's? Kaji addresses Misato as Katsuragi. Oh yeah, and Kaji.
In Fullmetal Alchemist, Lt. Colonel Hughes is referred to so rarely by his first name (Maes) that the casual fan or someone who hasn't seen very many episodes would probably only know him as "Hughes."
This seems to go for a good chunk of the military characters, actually. Even when screaming to each other in fear or pain in the manga, about 85% of the time or more, it's either the rank or the last name.
The only reason anyone would know Mustang's first name is the fact that Hughes seems to always refer to him on a First Name Basis. Roy also seems to be the only person to ever address Hughes as Maes.
There are two Armstrongs: Major Alex Louis Armostrong, and his sister General Oliver Mira Armstrong. Fans usually refer to Alex as "Armstrong", since he was introduced much earlier, and Olivier as "Olivier" (or "Olivia"). The series generally differentiates them by their ranks: Major (Alex) vs General (Olivier). Nobody in the series ever calls Alex by his first name (other than his sister).
Late in the manga, Hawkeye smokes out Envy impersonating Mustang by claiming that:
Hawkeye: When we're alone, the colonel always calls me 'Riza.'
Hawkeye:I Lied. Thanks for blowing your cover. *bang*
They almost exclusively use each other's ranks, only rarely bothering even with surnames.
The only person in the military who's most often referred to by his first name is Edward Elric. The only person who doesn't is Mustang.
Sakaki and Kagura from Azumanga Daioh are only known by their family names; no given names are ever shown for them, leaving fanfic authors with a few problems. (At least one fic has ended up having Kagura's father calling her just 'Kagura' in one scene.)note On the other hand, it's actually unclear if "Sakaki" and "Kagura" are last names, or first names. This was likely intentional, since these are the only names they're ever known by.
Also possibly worth mentioning, in the few scant minutes of screen time Ayumu had before being nicknamed after her hometown, she was called "Kasuga" by Yomi. Would she have continued to be called by her family name instead of her given name had Tomo not been quite so clever? The world may never know...
Signum of Magical Girl Lyrical Nanoha always refers to Fate as "Testarossa". Since Signum calls everyone else by their first name, and she and Fate are close friends, this seems to be treated as a term of endearment and/or respect for her long-time rival.
She continues to call Fate this after Fate's last name stops being "Testarossa."
Except the "Testarossa" name never completely disappeared; it just got turned into a middle name, usually rendered as just an initial (but explicitly stated at least once).
Vita also calls Fate "Testarossa." Shamal initially refers to Fate as "Testarossa-chan," but by StrikerS, starts calling her "Fate-chan."
In the StrikerS supplementary manga, Subaru initially calls Teana "Lanster-san," and Teana refers to her as "Cadet Nakajima" while explaining that they do not need to become friends. After Teana meets Subaru's sister Ginga and learns more about her, she decides to start calling her Subaru, claiming that it makes no sense to call her by her last name now that she knows her sister, and Subaru decides to start calling her "Tea". Erio and Caro initially have a bit of trouble calling each other by their first names.
An interesting use occurs with the Lieze twins; they request that Nanoha and Fate refer to them by their given names- Aria and Lotte- when addressing them individually, and calling them "Lieze" when speaking to both of them.
Youhei Sunohara of CLANNAD usually goes by his last name with the exception of his little sister Mei and Kyou. Then again, Kyou calls everyone by their first name.
It's also a subtle plot point in Kyou's route. Tomoya calls her Kyou but Ryou Fujibayashi, which she tries to get him to change because he feels he isn't as close to her as Kyou and loves her sister instead. He does start calling her Ryou, but... Well, it is Kyou's route.
In Mobile Suit Gundam Wing, Lucrezia Noin goes by her last name, and nobody, not even her romantic interest Zechs, uses the first unless they're calling her by her full name. (Fanon often has Zechs give her a cute nickname, such as "Lu", when they become a real couple.) This is actually by Noin's own request: when Treize tries to call her by her first name in a prequel manga, she actually corrects him and says that one's gender does not matter in the battlefield so he should make no distinctions in regards to her.
in Kare Kano, the two leads continue calling each other "Arima" and "Miyazawa" after they've slept together. They don't get to "Soichiro" and "Yukino" until a few months later.
Yu-Gi-Oh! has a lot of this. In the Japanese version and manga, characters such as KATSUYA Jounouchi and HIROTO Honda fit, and tend to only get their first names used by family. The tendency to refer to Kaiba by his surname carries over to the dub.
Bakura is a definite example in the manga and Japanese anime, with his given name being Ryou. The dub may or may not be an example as he is never given a second name, so it's possible his first name is intended to be Bakura.
Shuichi in Gravitation continues to refer to boyfriend Eiri Yuki as simply 'Yuki' (no honorific) even after learning that it isn't his real surname.
Naruto occasionally does this, with some characters, like Gaara, referring to Sasuke as "Uchiha." The Third Hokage is often referred to by his last name until his first name is revealed in the databooks, although in one translation, The Fourth Hokage calls him "Hiruzen-sama." Shiho calls Naruto "Uzumaki-kun", while referring to Shikamaru (whom she has a crush on) and Jiraiya (who only has one name) by their given names, so it's unclear to what degree she uses last names.
In the Suzumiya Haruhi novels, Kyon refers to everybody except Haruhi by their last name. In the ninth novel, he strangely also calls the mysterious interface, Kuyo, by her first name.
Kyon is confused as to which of Kuyo Suo's names is her given name and which is her surname when they are introduced, as she introduces herself in both orders; he calls her Kuyo-san most likely because that's what Sasaki calls her.
Also worth noting is that he never uses honorifics when addressing or speaking about anyone other that Mikuru Asahina. He also continues to refer to her as "Asahina-san" even though she told him to feel free to use her given name early in the series.
He does use honorifics with the upperclassmen (which Mikuru is), but it's almost always -san and not -senpai; in later novels he starts to refer to Kimidori as "Kimidori-senpai".
Most fans also refer to Itsuki and Yuki as Koizumi and Nagato, respectively. Speaking of which, Itsuki is almost never referred to by his first name.
Haruhi refers to the entire Brigade (including Yuki) by their first names, except Koizumi, which is probably why most fans ended up doing the same.
Several characters in the series aren't even given first names. Tsuruya, Kunikida, Taniguchi, Sasaki...
Yuki Nagato rarely refers to others by name in the main series, but in The Vanishing Of Nagato Yuki Chan, refers to most people by their last names, even calling her close friend Ryoko "Asakura-san", and most people refer to her as "Nagato-san".
In Bleach, Ichigo (Kurosaki), (Orihime) Inoue and (Uryu) Ishida are on a Last Name Basis with one another, including (Yasutora) Sado, though he does call Ichigo by his first name (Ichigo misread "Sado" as "Chad", so that more or less counts). Rukia is on Last Name Basis with the gang except for Ichigo and Renji. Ishida is on Last Name Basis with most everyone (excluding some minor characters), and the only people who refer to him by his given name in the original Japanese are his father and grandfather (and later Pesche). Following up on that, nearly every Shinigami in the series addresses the entire gang exclusively by their surnames, aside from Yoruichi (to Ichigo), Rangiku (to Ichigo, Renji and Orihime), Ikkaku and Yumichika (to Renji, Ichigo and "Orihime-chan"), and Kenpachi (with Yachiru; to Ichigo).
Captain (Toshiro) Hitsugaya is very particular about this, although he tends to insist that people also address him as a captain.
With or without addressing their respective ranks, most seated officers call one another by their surnames (such as Ukitake and Kyoraku), with the majority of the fandom following suit; aside from characters that are related by birth (the Kuchikis or Kotetsus), they call every other officer by their surnames.
Rukia Kuchiki's a bit of a complex case; because all of them outrank her, nearly everyone within the Gotei 13 (aside from Renji, Byakuya and Hanataro - the latter because she preferred as such) calls her Kuchiki, and due to her lone wolf demeanor at most points, she only (if ever) interacts with them while on-duty. Since Rukia's still a noble, if the -san (Mister, Miss, Mrs), or -dono (Lord, Lady) honorifics are in use, then they're being polite and respectful. As for Rukia herself, due to her upbringing as nobility, she tends to be respectful towards those of higher status or rank than her, addressing her superiors by rank and surname (i.e. "Captain Hitsugaya" and "Lieutenant Matsumoto"), sometimes with the -dono honorific (i.e. "Lord" Kaien and "Lady" Miyako).
Orihime herself tends to address everyone except Tatsuki by their last name.
When Ryuken Ishida calls Isshin Kurosaki by his last name with no honorific, Isshin says that's downright cuddly by Ryuken's standards.
The potential for this to be inconvenient is lampshaded in 473, when Hitsugaya is talking about Byakuya and Rukia Kuchiki.
Hitsugaya: I don't see Kuchiki and Kuchiki.
Ikkaku: Could you use their first names? It's a little confusing.
Katagiri's first name hasn't been mentioned. Everyone refers to her by her surname. For her part, being the Ishida family's maid, she doesn't even refer to Ryuuken and his parents by name at all (his parents are the Master and Mistress and he's the "young master"). She makes an exception for Masaki, however, by referring to her as "Masaki-sama".
The English dub performs a bizarre subversion mid-season. For the majority of the series, everyone refers to him as "Aizen," but in the middle of the Fake Karakura arc, without any explanation, the cast are suddenly on a First Name Basis with their most hated enemy.
In YuYu Hakusho, most characters call Kuwabara by his last name, except for his sister and Yukina. Shinobu Sensui tends to go by his last name most often, and this is significant because his first name changes based on which personality is in control.
The first episode of Digimon Adventure lists the full Japanese names of the characters, but Izzy (Koushiro Izumi) is the only one whose Americanised name is based on his Japanese surname. Even his parents call him Izzy.
Actually "Izzy" has a potential logical (albeit weak) explanation: when he was first learning to talk, "Koushiro" turned into "Izzy" (don't ask me how but it could happen) and it stuck.
The typical mode of address in Muhyo And Roji. Tohru Muhyo allows Jiro "Roji" Kusano to call him "Muhyo" instead of "Executor Muhyo".
Almost nonexistent in One Piece, due to relatively few characters even having last names, but some of Zoro's opponents call him Roronoa.
Though it can be noted that in One Piece pirate crew titles function much the same way as last names. Luffy's opponents rarely call him Luffy, or even Monkey (thank god, that would sound ridiculous) but instead lean towards calling him by his epithet, Straw Hat. Franky, who started out as a villain and got used to this, used to call him by that name. Other examples include Whitebeard and Red-Haired. Shanks switches abruptly to this from being on last name basis with Marshall D. Teach when he meets him for the first time since he has adopted the title of Blackbeard. Played straight with Rob Lucci, and a few other villains however. Ruthlessly averted with Garp and Roger, both of which always go by their first names, and no titles at all.
Shackey calls Luffy "Monkey-chan", and Smoker refers to a lot of pirates by their last name, for example Law and Ace. Interestingly, the three most recent characters with first and last names (Hody Jones, Ikaros Much and Caesar Clown) have been referred to with their last names (Hody, Ikaros and Caesar) as if they were their first names.
First Names are a rarity to begin with in Legend of Galactic Heroes, but absolutely nobody calls Yang Wen-Li by his given name (except his father, in a single flashback). Even his friends whom he calls by their first names call him "Yang." His wife just calls him anata (roughly, "darling").
Reinhard calls Kircheis by his last name because as a child he decided that it sounded better than his first name (Siegfried). Kircheis, however, calls Reinhard by first name (with the appropriate honorifics, of course).
An understandable standard in Monster, since most characters are in the professional field and do not know each other that well. The only person who ever seems to call (Kenzo) Tenma by his first name is his fiancee.
Kagami Hiiragi realizes how much time she spends in Konata's class after a short scene showing her own class calling her Hiiragi while Konata's calls her Kagami.
In Mahou Sensei Negima!, Kazumi Asakura usually goes by "Asakura", which is strange, given that practically everyone else in the class calls each other by their first names.
In Lupin III, (Arsene) Lupin the Third and (Daisuke) Jigen might as well have Only One Name for all the times anybody's used their given names in the show. Goemon Ishikawa the Thirteenth and Fujiko Mine, on the other hand, mainly go by their first names.
Otonashi, Iwasawa, and Naoi from Angel Beats!! are always referred to by their last names, even after their first names are revealed ( Yuzuru, Masami, and Ayato, respectively).
Surnames are said to be uncommon in the world of Dragon Ball, but the main character, Son Goku, has one. While most characters refer to him as Goku, his given name, Bulma, his first friend, refers to him exclusively by his surname. Piccolo and Tenshinhan often do the same but not always.
Except for a few racers and characters in Future GPX Cyber Formula, most of them are rarely called by their first names, like Naoki Shinjyo, Karl Lichter von Randoll, to name a few.
Yamato of Ultimo refers to his crush Sayama by her last name, and at one point, while thinking about what life with her would be like in the future, realizes that her name would not be "Sayama" any more.
The general rule between people in Bakuman。, even (so far) between Mashiro and his fiancee Azuki. Mashiro and Takagi refer to each other by nicknames while speaking with each other, but with last names when talking about each other to other people, such as their editors.
When Hiramaru gets together with Aoki, he notices that she's still calling him by his last name, while he uses an abbreviated and highly affectionate version of her first name. His editor claims that's proof that he's just a friend she has for tea, in order to manipulate him into becoming depressed enough to write well.
In Triangle Heart 3, most characters address each other by first names, but interestingly enough, Kyouya and Shinobu, the Official Couple, refer to each other by their last names.
Considering how close most of the Wandering Son cast is, it's odd that most of them refer to certain characters by their last names. To a new reader or viewer, you might even think the names are their first names, especially since several other characters are on a First Name Basis with everyone. Shuichi is always Nitori, Yoshino is always called Takatsuki, and Saori is called Chiba by almost everyone but Sasa.
Yurie in Kamichu! generally addresses Kenji as Ninomiya-kun, though she switches to Kenji-kun in the scene where she reaches out to rescue him from the typhoon she accidentally created. Unusually, the English dub retains this.
This is the standard way of reference in Kotoura-san, even between Haruka Kotoura and Yoshihisa Manabe, which are already having a stable relationship.
The titular Armitage of Armitage III. We find out fairly late in the series that she does have a first name, but no one ever uses it.
Cardfight!! Vanguard has (Toshiki) Kai, (Taishi) Miwa, (Katsumi) Morikawa, and (Yuuta) Izaki. However, we only ever learn Miwa and Izaki's first names in the credits. Meanwhile, everyone else is known by their first names (although some characters call Aichi Sendou by his last name).
In xxxHOLiC, both Watanuki and Doumeki are rarely if ever referred to by their first names (Kimihiro and Shizuka respectively). Doumeki himself never calls anyone except for Yuuko by their first name, (though to be specific, he never calls anyone anything except the first name he knew them as, as he'll continue to call girls by their maiden name even if they've married).
The Sweets Princes in Yumeiro Patissiere are on a last name basis with each other: (Makoto) Kashino, (Satsuki) Hanabusanote Ironically, played by the same voice actor who would go on to voice Aichi in Cardfight! Vanguard., and (Sennousuke) Andoh. While the latter two refer to Ichigo as "Amano-san", Kashino, being the kind of person he is, prefers to call her "Amano".