Basically, a girl has a boy's name. Frequently used to indicate some form of masculinity in the character; if not, expect the character to be very feminine and lament her name.
One commonly offered explanation for a girl having a Tomboyish Name is that her parents wanted a boy.
Many Japanese names are equally appropriate for men and women; tomboyish characters will frequently have one of these. At least two characters named "Megumi" were once boys, for example.
If the character is appearing for the first time, the others may have Pronoun Trouble, where everyone expects this Charlie Somebody person to be a guy, and are surprised when she isn't.
This can become An Aesop if said Charlie Somebody is in a traditionally male-oriented profession; for instance, the Step by Step episode where J.T. immediately dismisses female mechanics, before handing his car over to "Sam", who is apparently the best mechanic in town. The message can quickly get Anvilicious if done more than once in a series. Though you can hardly blame someone if the name means "male"/"man" or include "son" (see: Andrew, Charles, Benjamin).
Sometimes a variation of the Embarrassing First Name. Can potentially lead to Actually, I Am Him, and a good way to help disguise the fact that Samus Is a Girl until the right moment. The Super Trope is Gender-Blender Name.
This is a language-dependent trope: it's rather common in languages like English, but in others is impossible to do. For example, in Spanish most names have explicit masculine and feminine forms (and those that don't are either exclusively male or exclusively female), so this trope can't be used without it becoming extremely strained, to say the least.
One genre that is RIPE with this trope involve shows where a female is in an occupation that is typically considered a man's job (female cops, firefighters, soldiers, etc.) One of the most common is contrasting the incredibly girly Mackenzie with the very masculine nickname Mack.
Metroid bounty hunter Samus Aran could fit the trope as well. Of course, the manual for the original game says she's male (the decision to make her female came about halfway through the game's development), but Samus Is a Girl.
One also shows up in American Gods. Shadow asks her if she's a boy Sam or a girl Sam, because they were in the dark when she introduced herself and her voice was deep enough that he thought she could have been a preadolescent boy.
An episode of Family Guy had Chris make friends with a Sam who dressed in overalls and a hat, making him extremely confused when Sam kissed him. Of course it turned out to be a Samantha, but Chris was still kind of uncomfortable until she told him to think of her as a boy.
Alex on LOST, whose gender was not given until the first season finale. When we first learned of her, Rousseau simply said, "Alex was my child." In season 5, we learned she'd have been Alexander if she'd been a boy.
Alex D from Deus Ex: Invisible War. The name is purposefully ambiguous so that the player can choose to play a male or female character without needing voice actors to re-record their lines with a different player name.
The player's girlfriend in the Neverwinter Nights module series The Bastard Of Kosigan is Alexandra de Velan, who prefers Alex and serves as the brains behind an attempt to overthrow the leadership of the most important district of the duchy of Burgundy and have it defect to the French.
When Alex Meade on Ugly Betty had a sex change, she changed her name to Alexis, which makes no sense at all since both names are androgynous. Then again, "Alexandra" wouldn't have the same classic soap connotations.
In the Swedish 1950 film Girl With Hyacinths, the protagonist is trying to find out why a young girl killed herself. The only clue is the name of a lover, Alex. At the end of the film, the protagonist is rather stunned to discover that Alex is a woman.
Alex Forrest from Fatal Attraction; feminist criticism points out that the film has her punished for infiltrating environments traditionally reserved for men, with her name itself being an example.
Ashes to Ashes has DI Alex Drake. Gene Hunt had been expecting a male DI when he first saw her paperwork.
Wen Spencer's fantasy novel Tinker centers around a girl named Alexander Graham Bell. She prefers to go by her (also tomboyish) nickname, Tinker.
Anime and Manga
One of the oldest examples is Ryuunosuke Fujinami from Urusei Yatsura. Also one of the original Bifauxnen and a Wholesome Crossdresser to boot. As a rule, -suke is masculine, it's almost like -son (Jacobson, etc) in English. This is due to the fact her father is one of the most extreme examples of 'wanted a boy' in fiction - he forces her to act, talk, dress and pretend to be a boy when she wants to be feminine but can't manage it because of her upbrining.
There's a very boyish-looking girl named Edward on Cowboy Bebop, a very odd person who chose her own name (in full: Edward Wong Hau Pepelu Tivrusky IV).
According to her father, her real name is Françoise, which is nearly an androgynous name—it's exclusively female, but easily confused with its male counterpart François unless you know how French pronunciation works. Then again, her father is a bit unhinged and thought she was a boy when he was re-introduced to her.
Last Exile has a girl named Al (short for Alvis), and another named Alistair.
In Gundam 0080, the female pilot for the Gundam is Christina Mackenzie, which commonly is shortened to Chris in-series. The Gundam itself has a Tomboyish Name, Alex, but given that it is a robot, it doesn't invoke the trope.
Claes (a common boys' name in Nordic countries) from Gunslinger Girl was so named because her Handler didn't want to make his relationship with her "personal" by giving her a girl's name.
Petrushka and Rico are also boy's names, given to two other girls.
Oscar François de Jarjayes from Rose of Versailles - her father very much wanted a son and decided to name and raise her as a boy.
Baccano!! inverts this by giving a major male character the distinctly female-sounding name, Claire. This doesn't make him any less Badass.
The Dayof Revolution has a brother and sister named Makoto and Mikoto (Makoto is the girl.)...and a Gender Bender protagonist named Megumi as well, though in this case she actually pronounced her name "Kei" when she was a boy. (Isn't kanji fun?)
In Fruits Basket, Tohru is our main character. In a flashback, her grandfather wonders about her masculine name, and Kyoko says that Katsuya, her father, picked it to 'bring out her hidden flavor', like adding salt to something sweet to enhance the flavor. Also Akito has a man's name, but there's another reason for this.
Ukyo, from Ranma ½, is often mistaken for a boy when people first meet her. Her name doesn't help since it's male (although very old, so people might not know)
Ayumu from Life has a male name, which she hates for that reason and thinks doesn't fit her. She has short hair for most of the manga and can easily pass as a boy a lot of the time, but she's actually very feminine.
In Pokémon Special, while "Yellow" (Japanese pronunciation, ierou) is by no means a real name in any language, it sounds very masculine to Japanese ears, as "ie" and "rou" are both common suffixes to male names. Fittingly, Yellow goes around masqueradingas a boy for the first two arcs she appears in.
Seth of Trinity Blood. "Did your parents want a boy?" "I have two older brothers, you'd think they'd had enough."
In Archie Comics' Dilton's Strange Science, Teen Genius Dilton Doily invites a fellow prodigy named Danny to his house. True to the trope entry, he experiences Pronoun Trouble when he opens the door and discovers that his guest is a girl named Danni.
Come to think of it, Veronica's nickname also fits this trope, as "Ronnie" can be short for "Ronald".
Yukio in Marvel's X-Men books. That the ronin good friend of Storm uses a boy's name has led to speculation that it is not her real name. In the limited series Wolverine: Soultaker, her other good friend Logan wonders if her actual name might not be the similar-sounding, but unambiguously feminine "Yukiko".
After the death of Dark Phoenix, Cyclops left the X-Men for a time, and decided to apply for employment on a ship. The first person he sees aboard is a pretty young woman.
Cyclops: Excuse me, I'm looking for Captain Lee Forrester. I heard he was hiring crew.
Woman: My name is Lee Forrester — Aletys to my relatives — and you heard right.
In the 1980s Captain America fell in love with and for a time was engaged to Bernie (short for Bernadette) Rosenthal.
Parodied in Preacher with Tommi Ryder, a 'supermodel-turned-lawyer with a dangerous secret' protests that the 'i' makes her name feminine. Amusingly, her (male) love interest's name is Jody.
Barbara 'Bobbi' Morse-Barton, AKA Mockingbird, Former New Avenger, founding West Coast Avenger, and the exwife of Hawkeye.
In Welcome To The Jungle, Harry is thrown for a loop when the zookeeper named "Will" he's looking for turns out to be a woman. She says it's because she doesn't want to go by "Willamena".
In The Show That Never Ends, a Harry Potter fanfic, one of Harry's coworkers and Remus's eventual love interest is a woman who goes by Diz. It is later revealed that her full name is Disraeli Taylor; her mother was a historian. In fact, her sisters' names are Churchill and Dickens, and her brothers are Tennyson and Darwin.
A semi Tomboyish Name starts all the trouble in EuroTrip: The protagonist Scotty freaks out when his German pen-pal Mika Mieke comes on to him. Scotty reacted poorly because he thought Mika Mieke was a male name (along the lines of Mike/Michael), but it's actually a female name, roughly equivalent to Michelle.
Watts from the movie Some Kind of Wonderful. At the end of the first draft of the screenplay it's revealed that her first name is actually Susan, but this never happens in the finished film.
In the 1966 film This Property Is Condemned, one of the characters is a young girl named Willie (her parents wanted a boy).
In the comedy film But I'm a Cheerleader, one of the main characters is girl called Graham. Fits the stereotype by being a rather butch lesbian.
Randall "Randy" Dean, the butch teenage lesbian of ''The Incredibly True Adventures of Two Girls in Love", probably named after Operation Rescue founder Randall Terry by her very pro-life/anti-abortion mother.
The Howard Hawks/Leigh Brackett Western El Dorado (1966) has the very tomboyish Joey MacDonald (full name: Josephine), played by Michele Carey.
Evelyn as a male name wasn't completely unknown in the mid-20th century (most obviously, Evelyn Waugh), but it was pretty uncommon.
Arguably, Saavik in the Star Trek movies: there was a definite pattern to Vulcan names in TOS (men are called Spock, Sarek, Surak etc.; women are called T'Pau, T'Pring, T'Lar etc.) and she had a name that fitted the male pattern. (Since then, we've seen Vulcans whose names don't fit either pattern, but at the time...)
The character was originally conceived of as male, and wasn't switched to a woman until later drafts. They kept the name, though.
The eponymous character in Michael O'Hara the Fourth. Michael was the traditional first name of the eldest boy in each generation. When Michael O'Hara III's first child - a daughter - was born, he learned that his wife would not be able to bear any more children. Because "there has always been a Michael O'Hara", he named the girl Michael. In the movie, he says he thought people would would call her Michelle. Instead she is very tomboyish and everyone calls her 'Mike'.
In the Airhead series by Meg Cabot, the main character is geeky high-schooler Emerson Watts. She goes by the name of Em, mostly anyway.
Karrin Murphy of The Dresden Files goes by her last name. This is true in the TV series as well, although there she's a Connie rather than a Karrin. The change was made because Chicago's real-life police department contains an officer whose actual name is Karen Murphy.
Doctor Who companions in the Expanded Universe include Bernice "Benny" Summerfield (Virgin novels), Samantha "Sam" Jones (BBC Books novels), Isabelle "Izzy" Sinclair (DWM comic strip) and Charlotte "Charley" Pollard (Big Finish audios). This happens quite a bit in the Canon too, with Ace (real name Dorothy), Josephine "Jo" Grant and Melanie "Mel" Bush.
In Charlotte Bronte's book Shirley, the title character is given the name Shirley by her father, who wanted a son. This led to the name becoming a female name, and consequently modern readers need to be reminded of this. In fact, the book is the reason Shirley became a popular girls' name.
Inverted to amusing effect in Connie Willis's Uncharted Territory. A group of explorers learns they're getting a new intern named Evelyn Parker. The men are all excited to have a new woman in the group. Turns out that in Britain Evelyn can be a man's name, and Ev's parents were traditionalists. Cue disappointment from the men and snickers from the women, especially when it turns out Ev is young, handsome, and single. And straight.
The heroine of Robin McKinley's novel The Blue Sword insists on being addressed as Harry. It's not until halfway through the book that her real name is revealed as Angharad.
In Laurie King's mystery novels about police officer Katarina Cecilia Martinelli, she determinedly uses the nickname "Casey" on the job. Personal friends can call her Kate, though. And she's a lesbian, whose significant other is a female psychiatrist named Lee. It is not revealed until late in the first book, A Grave Talent, that Lee is female.
Max Ride is a girl. But you sure wouldn't know it if you watched her fight...
In one Berenstein Bears book, Sister Bear is being bullied by a classmate named Tuffy. Brother Bear heads off to give Tuffy a piece of his mind, is flabbergasted when he sees Tuffy coming out of the girls' bathroom, and quietly slinks away with her taunting him for not doing anything to her because he can't bring himself to beat up a girl.
Scout from To Kill a Mockingbird, which is her nickname - her full name is Jean Louise Finch. Needless to say, you only find that out in scenes where her aunt is trying to put her in dresses or other "formal" settings are happening.
The "oops, we wanted a boy" version occurs with reference to the name Nigella.
Inverted with the wizard Denephew Boot, so called because his 'simple country folk' parents wanted a girl, who they were planning to call Denise.
Sets up all the action in Swedish tween book Darfinkar Och Donickar Dårfinkar och dönickar]] (which translates roughly as "idiots and crazies", only the words used are very uncommon). Simone (French female name) is forced to move when her single mother finds a new man. Angry about it, she cuts off her hair. The next day, her new teacher introduces her as "the new boy, Simon". She runs with it.
Jack Starbright, housekeeper to Alex Rider (and the closest thing he has to family after his uncle dies). The first book mentions that Alex wonders what it's short for, but he never asks.
It's never commented on, but Beldaran in the prequels of the Belgariad. To explain it comes in two parts. The male disciples of the god Aldur get the prefix 'Bel' meaning beloved attached to their names while females disciples get the femenine form 'Pol.' Secondly the name without the prefix 'Daran' is used by her son and several of her descendants as a perfectly serviceable masculine name.
Mary Minor Haristeen, goes by "Harry" in Rita Mae Brown's detective series. Harry's official job is being the town postmistress, but she's also an Outdoorsy Gal and amateur sleuth whose dog and cat (Tucker and Mrs. Murphy) help her solve crimes.
Tom Gay (real name Lucinda Muriel) in the Chalet School books. And Joey Bettany, of course.
Malory Towers has both the series' heroine, Darrell Rivers, and late arrival Bill (short for Wilhelmina) Robinson, a very horsey tomboy who has six brothers and who quicky becomes best friends with the somewhat girly girl the Hon. Clarissa Carter.
Inverted in Enid Blyton's The Faraway Tree trilogy, the main characters are two sisters and their older brother called Jo - traditionally a girl's spelling. In later editions, it has been altered to Joe.
The title character of Catherine Gilbert Murdock's YA fantasy Princess Ben (it's short for Benevolence).
Temperance Brennen's sister Harry (Harriet) in the Kathy Riches series of crime novels.
Aunt Dimity: The Pym sisters' great-grandniece is named Aubrey Aroha Pym (she's descended from their older brother Aubrey Jeremiah Pym). She is commonly called "Bree."
In Remnants, Miss Violet Blake's birth name is Dallas, the city where she was born. Rather unfitting, since she's decidedly a girly-girl. Luckily changing one's name is extremely easy and common in this setting, even for teenagers.
Alias: Sydney Bristow, the main character. Her friends even call her "Syd".
Angel: Winifred "Fred" Burkle. In one episode, her name causes an old guy in Angel's body to mistake Angel for gay. Refreshingly, Fred is not sassy or conspicuously empowered (that role is taken by a character named Cordelia, itself an inversion of this trope).
Black Adder II: Nursie is revealed to have the first name "Bernard". She also has sisters named Eric, Basil and Donald. Nursie is not particularly tomboyish, but certainly is insane, so this all could be her imagination. "Bob", however, is tomboyish. Or tries to be. Of course, her name probably isn't really Bob.
Dark Angel: The female main character was named Max. This was also an Only One Name. Also, one season 2 episode had a girl named Ralph.
Dawson's Creek: The ultimate example would have to be Joey, who played the tomboy angle straight for the first couple seasons and grew increasingly girly as time went on. This is directly related to the Jo in Little Women, as this character is Joey's (and her mom's) favorite and the reason she's called Josephine like the girl in said book.
Dr. Quinn, Medicine Woman: "Doctor Mike," a.k.a. Dr. Michaela Quinn. There's actually a purpose to this, though. The writers felt it was necessary to explain why the townspeople accept the woman who is coming to be their doctor: they thought she was a man. Communication being what it was, her name was telegraphed to them, as telegraphs were, with no spaces, upper and lower cases, or punctuation. They're expecting "Michael A. Quinn." If her name had been Alice, or something, the viewer is meant to presume they would have cabled back saying "Forget it."
EastEnders has Ronnie Mitchell, whose name is a shortening of Veronica.
Eureka: Also has a Jo, who gets surly when people call her Josephina.
Extras: Somewhat parodied where Andy Millman goes to Ian Mackellen to audition for his new play. It ends up being a play about homosexual loves, something that is not apparent to him until "Fran" is revealed to be a man. Everyone in the audition room other than Mackellen and Andy appear to have tomboyish names if they are female or girl names if they are male. Things get ridiculous when one of the women in the room is referred to as "George".
The Facts of Life: Jo, while Jo-with-no-E is a girl's name, she was mistaken for a boy in the first episode, and is based off Jo from Little Women.
FlashForward (2009): Charlie Benford. It's unknown whether that's short for something more traditionally feminine.
Flashman: Pink Flash is named Lou!
Full House: There is DJ, who is the oldest daughter but the abbreviated initials are at best gender-neutral, if not leaning towards being boyish-sounding. It stands for Donna-Jo (not Joanna, not Josephine, just Jo).
Gilmore Girls: Lorelai Leigh Gilmore goes by the nickname Rory (a name which is usually reserved for boys) to distinguish herself from her mother and great-grandmother, both of whom are also named Lorelai Gilmore.
Harry's Law: Harry Korn looks like she'll kill anyone who calls her Harriet.
How I Met Your Mother: Has Robin Charles Scherbatsky, Jr., who practically embodies the "my dad wanted a son" excuse.
JAG: Sarah "Mac" Mackenzie, an officer and attorney in the US Marine Corps.
Jayma Mays: Played girls named Charlie on both Heroes and Ugly Betty in the same season. Not much chance for confusion, though, since while the UB Charlie is a recurring love interest of a main character, the Heroes Charlie was a one-shot who was killed off by the main villain. She was also the love interest of a main character though.... For the record, her full name is Charlene and in a later season, she comes Back from the Dead.
Liveman: Megumi Masaki was not only the first blue female, but the only female in dark blue tone. Funny enough, her actress is also named Megumi.
Mad About You: The characters Paul (male) and Jamie (female) are often referred to as "Paulie" and "James".
MAD TV: The Ditz Dr. Kylie Johnson was the victim of a typo at least once, or rather at least one of her patients was a victim of such.
Married... with Children: Gary, the owner of the shoe store where Al Bundy works, is a woman. Al spent his first twenty years of work at the shop believing she was a man. (He never met her until being told she'd come to inspect the shop. In fact, he once considered the possibility of Gary not even existing.)
Power Rangers S.P.D.: Takes this to absurd levels. Of the two primary female rangers on the show, one is "Z" (short for Elizabeth) and one is "Syd" (short for "Sydney"). They were a rather tough Tomboy and Girly Girl duo (with Z as the Tomboy and Syd as the Girly Girl), in some cases tougher than the boys, and Z is extremely tomboyish, Mama Bear regarding Sam the future Omega Ranger issues aside. It gets worse: On the A-squad, the end credits reveal its Red Ranger, female, to be named Charlie, and she's tougher still, and extremely tomboyish in mannerisms while still something of a Femme Fatale. She's either the best thing to happen in feminism in the franchise, or a Straw Feminist, depending on who you ask.
Scrubs: Elliot Reid, named after her father who wanted a boy. But let's not also forget that J.D. usually ends up sleeping with girls with androgynous names, including Alex, Dani, Jamie, Jordan and Kim. Might have something to do with the "lanyards" he made with his bunkmate at summer camp.
Elliot accuses another doctor of copying her because she, Veronica, starts going by the nickname Ronnie.
JD's original name was Joanna for the first three years of his life, as his parents were expecting a girl, and couldn't think of a proper boy's name for a while. While his name was changed to John, many of the jokes about him are about how stereotypically girly he is.
Sherlock: In this BBC series, John Watson's sister is called Harry. Having learned her name and the fact that she used to be married to a woman, Sherlock makes an almost accurate series of deductions regarding John's "brother".
Sisters: Had a whole family of masculine girl names: Alex, Teddy, Frankie, Georgie, Charley. However, this was not used to indicate masculinity, but that their father always wanted a boy.
Third Watch: Alex Taylor, a female firefighter who hates being treated differently due to being female.
The Vicar of Dibley: Had a female vicar called Geri (short for Geraldine), leading to confusion with traditionalist parishioners expecting a male vicar.
The West Wing: Josh was expecting a meeting from Joey Lucas. Not only is Joey unexpectedly female, but she's also deaf and has a male translater. There is some confusion as the translater says "I'm Joey Lucas" and nobody realizes for a little while that he's speaking for the deaf woman.
The Young Ones: Reversed with a male character named Vyvyan. When they go to the pub, where Vyvyan's mum is working behind the bar, Rick jumps at the chance to ask "Why did you give him a girl's name?" At which point Vyv smashes a bottle over Rick's head.
A rather famous inversion: Johnny Cash's Boy Named Sue. The original poem was written by Shel Silverstein.
In one Homer, the Reluctant Soul strip, Homer (who has been incarnated as the daughter of an Irish couple en route to Ellis Island) is about to be given a Tomboyish Name suggested by her Father... but her Mother, being more sensible, names her Honor (Homer's name during a female incarnation). Honor thinks to herself, "Drat. I kind of liked 'Fisk'".
WWE wrestler Mickie James is a former WWE Women's Champion. Granted, this is wrestling, and stranger things have happened than a man holding a women's belt, but she is a woman.
Former WWE ring announcer Mike McGuirk (real name Michelle).
If you heard the name "AJ," you wouldn't expect a cute young woman to come skipping out, would you? AJ fits the trope by being notably different from the standard WWE Diva in that she is seemingly sweet and innocent but enjoys traditionally boy things like comic books and video games, in addition to be a damn good wrestler who has been way into wrestling since childhood. ("AJ," of course, comes from her real name of April Jeanette.)
In the musical Once Upon a Mattress, Winnifred tells the Prince he can call her by her nickname. He guesses, "Winnie?" She corrects him, and a minute later, he's summoned everybody to hear his "Song of Love": "I'm in love with a girl named Fred!"
The title character of the George M. Cohan musical Billie. She and her show would be completely forgotten if George M! hadn't reused the title song, in which she divulges that her parents had wanted a boy.
In the late eighties, Hasbro created their own fashion doll line, with the title character being called MAXIE!
Reversed (sort of) in the Dating SimX-Change Alternative, with main character Kaoru. Since he is rather short of stature, rather pretty and... not blessed down below, it seems a little cruel of his parents to have given him a girl's name. Later on, it's revealed that he's genetically intersexed, so it's assumed his parents were just hedging their bets. Meanwhile, he's been gender bent...
Suikoden IV has Wendel, who gets mistaken for a guy by Nico, your ship's lookout. This is notable mainly because Nico's vision and perception are praised almost every time the subject comes up — in fact, Wendel has been trying to become Nico's apprentice because of his fantastic eyesight.
And yet another Makoto, from the IdolM@ster series, who becomes an idol in order to find a more feminine side of herself.
And Makoto from BlazBlue! Maybe this one's gaining ground as a girl's name.
Kairi. Though it is technically a gender-neutral name in Japan, it is really rarely used as a girl's name. Yet, the main Damsel in Distress of the game Kingdom Hearts has this name, and she displayed a somewhat tomboyish personality during the periods in which she was conscious.
For a male example, Axel's true name before turning into a Nobody was Lea.
Actually, it was just a variation of "Lee," which is usually masculine.
Harold Berselius of Tales of Destiny 2, who is in fact often mistaken as a man by people who have yet to meet her.
And then there's Corrine, the summon spirit in Symphonia. Corrine is typically a female name, and the spirit itself has a high-pitched, feminine voice. However, there are some instances Corrine is referred to as male, as well as taking into account that Corrine would eventually become Verius, who is definitely male in name and voice. This is even more confusing as what Corrine's relation to Verius is never agreed upon in Symphonia's many iterations as sometimes Corrine is a different persona from Verius and could potentially be female when Verius is male, or Corrine is Verius where Corrine could have been too young (in voice) to pass as a young male rather than outright female.
In Mass Effect 2, one of the teammates that Shepard must pick up is a convict named Jack. When you release Jack from cryo-stasis, the other party members are surprised to find a shaven young woman of a smallish frame covered in tattoes and little else... Who proceeds to single-handedly go on a Roaring Rampage of Revenge across the ship and tear it to pieces.
One of Mana Khemia 2's playable characters is the tomboyish Et, short for Etward. As a child, she decided her little brother's name was better and forced him to switch with her. The fact that this typifies his relationship with her and he grew up as Enna (short for Ennarcia) is only the start of the poor kid's problems.
Chromie from World of Warcraft is a bronze dragon who preferred lesser form is a female gnome. While most female bronze dragons have names ending in "ormi" her full name is Chronormu, and "ormu" is the ending associated with male bronze dragons. This led many to speculate that she was in fact a male dragon who preferred to take femmale shape (which, given the game, would be wholly appropriate) but Word of God eventually clarified that she just had a Tomboyish Name.
Makoto in Kanon is called out on having a "boy's name". She did take the name from someone else, but that person was also a female.
This was actually a plot point in the final case of Phoenix Wright: Ace Attorney: Justice For All. A female character is accused of murder when the hired gun who did the killing names her as his client. He makes a crucial mistake when he claims that he met his client in person and calls the client a "he". The woman has a masculine name (Adrian Andrews). Phoenix points out that if the killer had actually met Adrian in person, he would've called her a "she".
In the opening sequence of Go! Go! Nippon!, the (male) main character reflects on how he's taking his first trip to Japan and that he'll be staying with two brothers, Akira and Makoto, who he met in an international chat room. Only after he arrives and meets them in person does he realize they're sisters. Makoto even lampshades this, admitting that Makoto and Akira are more common as boy's names.
Three of the four (formerly male) main characters in Cheer! have gender-ambiguous names (Sam, Jo and Alex), even though these are all different from their original male names.
Parodied in Schlock Mercenary: when Captain Tagon decides to hire a new medical officer, the first thing he notices are her rather large physical assets. He only notes that her name is 'Edward' (due to her incredibly stupid parent's poor choice of names) after deciding to hire her (but before actually looking at her professional credentials).
Ariel (pronounced as the more masculine R-E-L rather than Air-E-L) from Drowtales, ironically, she is sent to a boys school (because of exceptional circumstances) and one of her (male) classmates is more effeminate than her. Also, it later turns out she is blessed with shape shifting abilities, so she could basically be anything, though her attempt to do "something interesting" and make herself physically male with them didn't work.
There's also Chrys'tel, who's usually just called Chrys, but only by human standards. She's not particular tomboyish, however.
Wapsi Square has Bud, which is luckily a nickname. Her actual first name is Acacia, which doesn't shorten well, so she goes by a shortened version of her last name (Budur).
In a flashback, Tangerine of Sinfest rejected girlie stuff and the name Angie to climb a tree and call herself "Tange".
Billie Wilson, who actually is a tomboy, in the Whateley Universe. Since she also hangs with Toni Chandler and Nikki Reilly, this could cause problems if they weren't all hot superheroines. And Sam Everheart, extremely-competent female security officer at Whateley Academy, with her own secret to hide.
Not really a true example since all four of these characters are former boys who chose feminized versions of their former male names or nicknames as the case may be.
Codex from The Guild has the real name Cyd. She specifies that it's not short for anything.
Tex from Red vs. Blue. It's short for her codename, Agent Texas; her real name Allison is a lot more feminine.
With Killerbunnies, along with being gender blender names, have Thomasina "Tommie" Evans and Mikie, which like the Mike, Lu & Og example, is short for Michealenne, both of which are feminine forms of the males names Thomas and Micheal.
We also have Milo, which is typically seen as a boy's name, unless one takes into account it is pronounced "Mee-loh" and is Hawaiian for "hibiscus", a kind a of flower.
6teen: Nikki Wong embodies this trope. Short-cut, purple-dyed hair: check! Grungy wardrobe: check! Sarcastic sense of humor and badass personality: Double check! Name that can apply to Nickolas but instead applies to Nicole: check!
Batman: The Animated Series: In one episode, Poison Ivy appears to have gone straight and gotten married. Batman observes some heartwarming interactions between Pam and her stepsons, Chris and Kelly, but realizes something's up when Robin says he knows the "husband" and his daughters.
Subverted in Recess with Spinelli, a tomboy who goes by her last name because she's embarrassed about her "girly" first name, Ashley. It's especially "girly" on this show because there's a club consisting entirely of Alpha Bitch girls with this name (who seem to equate the name with popularity), and one episode was about the consequences when the Ashleys found out her real name and forced her to join their club. Ironically, Ashley was once considered a boy's name (such as in Gone With the Wind), and some well-known guys do have Ashley as a name (like Ashley Cole). Sometimes, they go by "Ash".
You mean Reggie wasn't her legal name? Huh; that's weird; I knew a girl whose legal WAS Reggie.
Total Drama Island stars Izzy, which may or may not be short for Isabella. Revenge of the Island has Jo, who is a straight-up tomboy, disliking anything even remotely girly and is often confused for a guy by Dumb Jock Lightning.
What's New, Scooby-Doo?: In one episode, the guys on the gang are excited about meeting a pair of male roller-coaster designers called Chris and Terry, while the girls are unimpressed...until they turn out to be sisters called Chris and Terri.
W.I.T.C.H.: The leader of the Guardians, Will Vandom, is a girl like the others. Depending on the source, it's short for Wilma, or Wilhelmina.
A bizarre twist on this trope: over the last hundred years, Ashley has gone from being a male name to a female one. (Not to anyone who has seen Gone with the Wind)
As has Meredith, though that could be more the transition from Wales to the U.S. than time...
Not to mention Madison; the name's popularity as a female name has been credited to its appearance as a name chosen by the mermaid in Splash.
As mentioned above, Shirley was a distinctly male name until 1849, when a book came out featuring a female protagonist who had been named Shirley (because her father had wanted a boy), thereby popularizing the name for girls instead.
Andrea is a very common men's name in Greece (Shares a root with Andrew) and a not-very-common-but-not-unheard-of girl's name everywhere else. The root of the name? Greek for "man"...
"Lee" and any names that end in "-lee" or a variation thereof were at one point exclusively male.
When Howard Hawks hired Leigh Brackett to co-write the screenplay for The Big Sleep (with William Faulkner), he was surprised at their first meeting to find the writer he hired was a woman.
There's a well known human rights lawyer in Britain called Gareth Peirce, although she changed her name legally. "Gareth" was originally her middle name.
Cayman Ilika, named for the Cayman Islands, where her parents spent their honeymoon.
Justifiablely averted in Germany where parents are banned from assigning names that doesn't clearly designate their child's gender.
Can still happen with middle names. Just ask actor Klaus Maria Brandauer or comedian Markus Maria Profitlich.
Not uncommon in some countries for Roman Catholic men to have María as a middle name. See also German author Erich Maria Remarque (who changed his middle name in honour of his mother), Spanish politician José María Aznar, Spanish golfer José María Olazábal, French politician Jean-Marie Le Pen. In this case, however, "José María" is considered a "compound name", as both names will be used together. If someone referred to Mr. Aznar as "María Aznar" or even "J. María Aznar", people will assume the speaker is referring to somebody else (a female).
In Spanish, at least, the combined name "María José" is also common. Again, it's exclusively a female name.
ESPN Sportscenter anchor Chris Mc Kendry is a woman as is MSNBC anchor Chris Jansing.
TheBogarts named their daughter "Leslie Howard Bogart" after the late Leslie Howard, who insisted to the studio that Humphrey Bogart reprise his stage role in the movie adaptation of "The Petrified Forest", which boosted his career.