A Bokukko is a female character who uses male pronouns. This term arises from the Japanese Pronounboku, primarily used by boys and young men, and "ko", a feminine suffix. Extreme tomboys may prefer the pronoun ore, normally used by Hot-Blooded young men. (This, incidentally, is an example of how Japanese writing differs from Japanese speech; although feminine speech patterns have by and large become more "neutral" over the years, it would still be quite unusual and out of place for a woman to refer to herself with a masculine pronoun.)
Like many of the "-kko" terms, this has its place in female archetypes in anime or Japanese Video Games. Most, but not all, bokukko are tomboys, and not all tomboys are bokukko, as the term revolves solely around the use of the pronoun "boku". Sometimes, it can just simply indicate that the user is a Plucky Girl.
While the use of boku most often signals tomboyishness, it can sometimes signal some other situation, such as not knowing correct societal behavior, or lacking polite speech. Sometimes it can be used to keep a characters gender obscured—is she a boyish girl, or a girlish boy?
Whenever a Bokukko that primarily uses the male pronoun permanently switches to primarily using the female pronoun, it's a plot point. When the show is dubbed, however, this will invariably lead to a Dub-Induced Plot Hole due to the lack of gender-specific first person pronouns.
Also, a Bokukko character will usually be addressed with the "-kun" honorific.
Although none of this has to be reflected in her appearance, the bokukko is usually either flat-chested or extremely well-endowed. A Dark-Skinned Redhead is likely to be a bokukko, but it's not guaranteed.
See also Cute Bruiser, Shorttank.
In Haruhi Suzumiya's 9th novel, Sasaki is introduced in a flashback. The reader isn't told her gender until later in the flashback, relying on her speech patterns (she talks a lot like Koizumi) and the use of masculine pronouns. The reader, confused by Haruhi's behavior around this "very close friend" of Kyon's, suddenly understands. As it turns out, that doesn't translate too well into English.
There's also an illustration of her before she even meets Haruhi; she's wearing a skirt and looking very unambiguously female.
Sasaki is an interesting case; she uses male speech patterns with boys, but feminine speech with girls. It's currently unknown why she does this; Kyon's best guess is that she believes romance is a waste of time and tries to seem masculine around boys so they subconsciously think of her as One of the Boys and don't become attracted to her.
Ryougi Shiki after the car accident from Kara no Kyoukai. Also note that she uses ore instead of bokuin order to imitate her lost male persona. At the end of the seventh movie, she switches back to watashi upon accepting the loss of her male persona.
Akito Sohma from Fruits Basket addresses herself as boku. This is largely because she was forcefully raised as man by her mother, and acted like one until she was about 20.
JunJun of the Amazones Quartet refers to herself with ore. She is also the only member of the Quartet to wear pants (of course, this being the Amazones Quartet, the pants hardly count as pants and you'd be hard pressed to find a guy who would want to wear them, but it still counts for something, right?) According to Naoko Takeuchi, she also talks like a yankee and is a biker chick.
Haruka a.k.a. Sailor Uranus uses the "boku" pronoun. Mamoru even refers to her as "Haruka-kun" because of her boyish personality.
In Bleach, while the tomboys tend to use the girlish atashinote (Karin, Tatsuki) or uchinote (Hiyori) pronouns, there are some genuine bokukkos:
Yoruichi's cat form is often mistaken as male because of the way she refers to herself/voice in anime. She uses the old sounding washi and the cat has a deep male voice.
Kuukaku Shiba has a rough personality that's emphasised by her use of ore when referring to herself. It goes with her masculine name.
Giselle Gewelle is a young woman who actually uses boku. She is accused by Yumichika of being a Creepy Crossdresser. While she doesn't outright confirm or deny it, she identifies as female, and is VERY angry with Yumichika for pointing it out. (Plus, Mayuri refers to Giselle as female, and heshould notice something going on).
Liltotto Lamperd is a rude little girl who uses ore.
Hilariously inverted with Urahara, a male who actually uses... atashi to refer to himself. His use of it exaggerates his role of a 'humble' shopkeeper. (In the flashbacks, he seems to have been more of a boku user)
Souseiseki from Rozen Maiden, although she's more stoic than brash.
Ryuunosuke from Urusei Yatsura. "Ore wa onna da zo!" ("I'm a woman!") Lampshaded and made more ridicolous by the resident Ataru and Mendo trying to teach her to talk like a girl and showing themselves really proficient at it.
Also by Rumiko Takahashi, Ukyo Kuonji from Ranma ˝ uses the word ore to refer to herself. She's also the most boyish of the fiancées (i.e., she goes to school wearing the boys uniform, whereas Akane uses the girls one), but according to Ranma she's still the "cute one" among them. In the anime she once entertains the thought of acting more feminine (she does indeed wear the girls uniform and looks very cute in it) to try attracting Ranma, but by the end of the episode she decides to just be herself and drops it.
Akane Tendo is a subversion: she is not a bokukko and in fact has rather girly speech patterns and tastes, but almost everyone treats her as if she was a tomboy. Kuno even refers to her as "Akane-kun", which she really doesn't like.
Kei, the more tomboyish half of the Dirty Pair, tends to devolve into this style of speaking whenever she gets particularly angry. In Dirty Pair Flash, she even said "Ore wa onna da!" at least once.
In Revolutionary Girl Utena the titular character uses "boku". In the movie, she's actually mistaken for a guy (despite her bright pink hair). In the TV series, Utena's tomboyish qualities are at times acknowledged by other characters as defining traits for her. One episode (set after Utena's loss in a duel with Touga) explores what a more feminine, Yamato Nadeshiko Utena would be like (and her fangirls were still wet for her). After Wakaba delivers her a Get a Hold of Yourself, Man! since she realizes how Utena's trying to be someone she simply is not, she eventually abandons this in favor of returning to her usual attitude and winning Anthy back.
Akira Sakou from Girls Saurus actually has some very complicated gender identity issues, and dreams about being a boy every single day. Consequentially, she doesn't have a problem with boys seeing her naked and sometimes uses the boys' bathroom... but in a bizarre inversion of Sitch Sexuality, becomes attracted to Shingo because he's the only person who's afraid of her. What's more, she lives in a Big Fancy House and is a total (explicitly identified) Yamato Nadeshiko at home, which only complicates matters further.
The fact that her attraction to Shingo resembles nothing so much as an athlete being attracted to a teammate doesn't make matters simpler, either.
Strangely for the sheer number of girls in the story, Mahou Sensei Negima! doesn't seem to have one among the main cast. There is only the very minor character Fuka Narutaki, who is described by Akamatsu as being the tougher and more boyish of the Narutaki twins.
Austria and the Holy Roman Empire thought Italy was one when he used to use "boku" to refer to himself in the days everyone thought he was a girl. (It's hinted that Hungary either always knew or realised it by herself, but kept her mouth shut). He has switched to "ore" since then.
Actually, the closest to a canon bokukko is... theveryfeminine Monaco, who is said to have speech patterns akin to an old man's.
Moemi Hayakawa invokes the trope when she cuts her hair short and starts acting and speaking more boyishly to make herself look more appealing to Youta. It doesn't work. In the end, she keeps her hair short but returns to her Yamato Nadeshiko self.
Ursula from Kiki's Delivery Service is pretty much textbook bokukko. A girl in her late teens living on her own during the summer in a cabin in the woods, Ursula is the embodiment of the strong-willed independence commonly desired by Japanese girls. Those attributes do make her come off as somewhat of a Tom Boy, but her choice of attire leaves no doubt she's all woman, except when a stranger giving her and Kiki a lift into town said she had "boy's legs". Her response to that was more of "Some people..." rather than indignation, indicating she's quite comfortable being bokukko.
There's always Yu-Gi-Oh! GX's Yubel for a rather creepy example. Technically, Yubel is more of a he/she considering the whole hermaphrodite thing. However, s/he's constantly proclaiming her love for Judai, and was originally a human girl.
A Zig Zagged Trope in Wandering Son. Takatsuki Yoshino is a female-to-male pre-teen trans person, and everybody refers to them as Takatsuki-kun. Subverted when they went on town with their friend Nitori, a male-to-female trans person, and they (Yoshino) noticed that they still uses "boku" when talking, even when wearing a dress. Yoshino says it suits them (Nitori) and says that they'll continue to use "watashi" despite dressing like a boy.
A meta example happens with Nitori. As said above she identifies as female, and is quite a Yamato Nadeshiko, however she still refers to herself as "boku". She explains it's just because she likes it and thinks it fits her.
In Darker Than Black Ryuusei no Gemini, Suou Pavlichenko, the new female protagonist uses Boku. This doesn't help the fact that the she looks almost the same as her twin brother if she is hiding her hair
Ookami-san's Ryoko Ookami, who fits both the "masculine pronoun" and "tomboyish appearance" parts of the trope.
Yagyuu Kyuubei from Gintama- it was used to conceal her Bifauxnen throughout the arc in which she was introduced.
Tatsumi, the fire fighter, uses "ore" and also refers to herself as "onii-chan" when speaking to children. It's likely that she adopted this way of speaking due to being raised in a very masculine environment; her adoptive father believes that women can't be fire fighters, but Tatsumi still idolizes him and wants to follow in his footsteps.
Tomonori/Yuki/Maelstrom from Kore wa Zombie desu ka?. In fact, her speech patterns, not just the pronouns, are entirely like a boy's, so much such that initially, Ayumu mistook her for a guy. The reason why she's called Tomonori is because it's how you would read the kanji of her name, if it was a guy's name.
Touhara Asuha from Lotte no Omocha, justified because she was raised by her single father.
In Binbo Gami Ga we have Ranmaru. But instead of "boku" she uses "ore".
In Ouran High School Host Club, Haruhi refers to herself as "boku" for obvious reasons, but she was already tomboyish before that. Actually there was one panel in the manga where she considered referring to herself as "ore" in front of the guests. In the anime, this was translated more or less like "Maybe I should call everyone bro and dude from now on?" and of course, Tamaki's reaction was...his usual reaction.
Actually, Haruhi starts the series referring to herself as jibun. It makes sense since jibun is technically gender-neutral (though often used by men in the military), so is often used to "mask" a character's gender.
The protagonist of Ice Revolution is an androgynous girl who uses "ore". In an attempt to seem more feminine she begins ice skating.
Hajime Ichinose from Gatchaman Crowds uses "boku" in addition to several other non-standard speech patterns. Unusually, Hajime is a very feminine character, so this probably isn't to sound masculine at all and instead highlight how odd her manner of speech is in general.
La Roux - The name chosen by the the band's singer; a mixture of "la rousse" (redhead female) and "le roux" (redhead male).
Hitomi Yoshizawa, from Morning Musume, does not use the masculine pronouns, but it's been noted by other members and persons in talk shows that the rest of her speech is quite masculine
The (unnamed) protagonist of the song Revenge Syndrome. She refers to herself in the lyrics several times using the "boku" pronoun. Not much is known about her other than her unstable mental state and her tendency to be bullied by her peers.
Gemini Sunrise from Sakura Taisen V uses "Boku" in the Japanese script. In addition, her twin sister/dual personality Geminine uses "Ore".
Princess Tailto from FE 4 aka Seisen no Keifu, too. Her speech patterns are rougher than the other women in Sigurd's army, though it's not really alluded to by other charas. She is very straightforward when compared with the other girls save for Ayra, though.
It's explained in The Legend of Zelda: Twilight Princess that the character of Ashei was raised by her widowed father, an exiled knight, who basically treated her as a boy. She's a really good warrior, and cute with a nice figure, but doesn't know much about social niceties and is a little self-conscious about it.
The Justice refers to herself as "boku" in the Japanese version of Magical Drop 3. Fittingly, she's a tomboyish Action Girl.
In Touhou fanon, Wriggle "I'm a girl!" Nightbug gets this treatment quite a bit, due to her androgynous appearance.
Although Marisa Kirisame behaves tomboyishly and ends her sentences with "ze", a masculine sentence end which indicates force and command, she doesn't use "ore" in canon, as she's known to do in doujinshi.
Yggdra Union, Blaze Union, and Yggdra Unison have Emilia, who otherwise uses feminine speech patterns. Given her background, she likely was never taught to use a different pronoun while growing up, and since her brother is now Emperor, no one's going to tell her not to speak the way she wants to.
Gloria Union has Pinger, who actually uses keigo. Justified in that the person who raised her wanted her to be a marketable rarity, and may have trained her to have a weird speech pattern to increase her worth.
Razzly from Chrono Cross refers to herself as boku, possibly because she's the closest thing the game has to a male fairy (who are all female). Kid uses ore while calling herself a "cute, frail girl" in one breath.
Margie/Marguerite from Xenogears. Ramsus likewise addresses her as "Marguerite-kun."
Junko Enoshima is a rather odd example. She normally uses the super-girlish atashi... but when she's revealed to be the Big Bad as well as being such a Mood-Swinger that her entire voice and personality changes with her mood, her "punk" personality uses the very manly ore.
Chihiro Fujisaki uses boku at times, which is kind of odd considering that she's a timid little girl. Later subverted, since it's revealed that he's actually a timid little boy.
In Higurashi: When They Cry, both Hanyuu and Rika Furude use "boku". This is despite the fact that neither fits the normal pattern for the trope, though in Rika's case, it's probably a habit acquired from Hanyuu. She also uses "watashi" whenever she's not Obfuscating Stupidity. Hanyuu, on the other hand, only uses boku because she's Really 700 Years Old and comes from a time when boys and girls apparently didn't use different pronouns.
The very female Nya from Demonbane uses masculine speech. It's an early clue that she is not actually a woman... or even human, for that matter. "Nya" is not one of Nyarlathotep's more imaginative aliases.
The voice actress Akeno Watanabe uses boku in real life. And voices many tomboys, too.
While it's very rare, some real Japanese girls do use masculine pronouns. Those who do so fall into three types—girls who use them as a feminist statement/are just plain tomboyish, those who do it to imitate anime and game characters to be cutesy, and very young (preschool-age) girls who haven't been trained to use traditionally feminine pronouns by societal expectations (the more cynical may think of it as "gender policing"). The Japanese page on this phenomenon on The Other Wiki notes that this is a very recent trend. See also this case study on use of boku vs. use of watashi in young girls.