Dragon Ball is notorious for this. It started with a cast of a girl and a boy, later adding males Yamcha and Oolong and (maybe) female Puar. The males started to outnumber the females later, where against all the fighters in the cast there were only Chi-chi and Launch, and then the latter was forgotten.
Videl and Android 18 are the first regular characters to also be regular fighters alongside the male protagonists. In addition, Android 18 started out being the first serious female villain in DBZ (alongside her twin brother, Android 17). Ch-Chi did fight some toward the end of the original Dragon Ball, but she was never regularly in this position.
In Ghost in the Shell, the only woman is Major Motoko Kusanagi, but she is both The Protagonist and The Leader. Justified due to the fact that, while speculative fiction, it preserves the country's real world issues. Sexism in the government is dealt with explicitly later in Stand Alone Complex, and is a major catalyst for many of the political issues encountered later. Given this attitude, it's not unthinkable that an Elite government operations unit would have difficulty maintaining women not hyper-competent.
Mazinger Z: Sayaka Yumi was the only female main character (albeit, unlike other Smurfettes, she demanded being taken seriously like her own individual) and the only recurring female character until Misato appeared in the last season. Between the bad guys, The Dragon Baron Ashura may or may not count like female character. Dr. Hell mostly "hired" males (let's think of it, it can be infered from his backstory he had actually come to loathe women), but every so often he made Robot Girls or female androids Minerva, Erika, the Gamia triplets, the robots impersonated Hitomi and Kouji and Shiro's mother...)
Great Mazinger: Jun Hono was the only female character between the heroes (and Marquiss Janus the only female member of the Mykene high command. Then again, the remainder members were humans whose brains had been grafted into Humongous Mecha, so it was hard telling). That changed during the last chapters, when Sayaka was Back for the Finale and the male to female ratio became 3:2. In the Gosaku Ota manga, Misato again was a recurring character in the last arcs, so the ratio became 3:3.
UFO Robo Grendizer: Grendizer played this trope with Hikaru until the third season when Maria joined the team and the gender ratio became 2:2.
Naruto enforces this trope religiously, regardless of the size of the group. There is one female in every Genin team (that matters), there is one female among the five Jonin senseis (all the ones we've seen that aren't teachers are male), there's one known female member of ANBU, there is one female among the three Chuunin Exam proctors, there is one female among the Sound Five, there is only one female among the Akatsuki, only one female in Snake/Hawk, and there's even a single female Pain body and even that was a replacement for another one that died. We might as well call it "The Kunoichi Principle".
There has been one recent group that is an exception: the Cloud village team taught by a man named Killer Bee (the host of the eight-tailed beast) is the first to have two girls (Karui and Samui) and one guy (Omoi), although arguably, that squad is one person short since Samui is the squad's leader, a position equivalent to Kurenai/Kakashi/Gai's.
Although this can be read as there being a 2:1 male to female ratio, thus making 1/3 of the main and secondary characters female and therefore averting this trope - 1/3 of a large cast is much more than one.
Also, Kishi has obviously been trying to remedy this lately - For example, there are two females amongst the Jinjuuriki, two of the five Kages are female, he introduced Shiho the investigation squad girl, Naruto's Mother and the first and third Hokage's wives... . Note that the lone Akatsuki woman fought on par with the Big Bad, and while the girl in Taka/Hebi wasn't much of a combatant, her abilities were by far the most useful, given that their leader already had more than enough raw combat power on his own.
Record of Lodoss War has a typical fantasy adventuring group which is mostly male. The sole female main character is a blond elf named Deedlit (keep in mind that this series was based on an actual Tabletop Games campaign played by a bunch of Japanese college fraternity brothers in the late Seventies — women didn't always fit well into hack'n'slash scenarios).
The sequel Chronicles of the Heroic Knight averts this. The "new generation" of heroes consists of three (or four) male and three female characters. As with the previous heroes, Shiris was given a bigger role, and former Faux Action Girl Deedlit was markedly more competent — both had to save the male heroes more than once.
Inverted in Azumanga Daioh - there are only two male characters (three if you count The One Guy) with a notable role in the series. Every other main character in the series is female; the gender ratio is 1:5 or 3:10.
In Saint Seiya Omega, Aquila Yuna is the only girl among the Bronze Saints. And on the contrary of the usual series' history where women are mostly not very competent, being the only girl doesn't exclude Yuna to be a highly competent Action Girl, equally capable of accomplishing feats of badassery that other boys in the series are capable of.
Voltron (Golion) also has one heroine in a squad of heroes. Dairugger XIV didn't have that much better a ratio either, with roughly three females in three squads. Notably, Princess Allura originally only joined the team as a replacement after one member of the all-male Five-Man Band was killed. Even then, it was over everyone else's objections, and only because they couldn't form the Giant Robot without a fifth member.
That said, Princess Romelle could be seen as an additional female character, even though she doesn't make her debut until Episode 17, and a more kick-ass one than Allura. (Unlike the former, Romelle actually 'fights back' against would-be attackers.) Queen Merla was added by the American writers/editors of the series for the second season that got distributed to the Western market.
Uchuu Senkan Yamato has — you guessed it — one heroine in a squad of heroes. Early episodes showed more women among the crew, but they all abruptly disappeared.
Gundam uses this to varying degrees from series to series. Examples:
Gundam Wing has a roughly 1:1 male:female ratio, but few of the woman are pilots and even fewer are main characters.
Gundam 00 has at least a high frequency of female members, but none is a pilot (depending on your opinion on Tieria, that is). At least one is a high ranking officer and one is a capable pilot.
There is Chall Austica of manga-only 00P fame.
G Gundam, which mainly is about a fighting tournament, has one female participant shown, and a handful of other female members....about half of which are part of one character's cheerleading squad. They act as his support crew too, but it's sort of difficult to remember that they're supposed to be highly skilled engineers when they're being paraded around in bathing suits for no particular reason.
UC makes things more complicated. Mobile Suit Gundam had a fair amount of female characters, but only two were mobile suit pilots, one who wasn't very good and one who was also the main character's Love Interest. However, Zeta and ZZ were much better about this: Zeta had about as many female elites as males (Emma, Reccoah, Sarah, Fa, Rosamie, Four, Lyla, Maua, and Haman of course) ZZ had about the same quota (Elle, Roux, the Purus, Chara, etc), also Lady of War Haman got the part of the main villain throughout the bigger part of the series.
A major female character in the first Gundam series (Sayla) was planned to be far more important in the storyline before her voice actress died unexpectedly.
Gundam Sentinel take it to another level, the only active female character is ALICE, and she is mobile suit's AI. She has personality of little girl, but no humanoid appearance, not even avatar image on screen. On other hand, she has more Character Development than The Hero and make you wonder if the latter's just a Decoy Protagonist.
In Yu-Gi-Oh! the only female character to be around during the show's entire run is Anzu among a group of Yami Yugi, Yugi, Jounouchi, Honda, Kaiba, Mokuba, and to an extent Bakura and Otoji. Mai and Shizuka put in appearance now and then but are really secondary characters.
In the spin-off Yu-Gi-Oh! GX it gets even worse - Asuka is the only girl among Judai, Sho, Ryo, Manjoume, Daichi, Ed and Tyranno. The only other female cast member to get more than a few episodes was Rei, who didn't join the cast until the third season and even then didn't get a lot of screentime in comparison to the rest of the cast.
The director of Mai-HiME claimed in an interview that he deliberately wanted to invert this trope. Indeed, the important male cast is considerably smaller than that of the female cast. But considering that this a Magical Girl team show, the effort's kinda misapplied.
One Piece has two female Straw Hats (with one temporary member), one female Supernova, and one female Warlord of the Sea, one female Giantnote who is also a Marine, and one Celestial Dragon. Furthermore, one of the four emperors, Big Mom, is female.. Most of the evil organizations have exactly one female member, whom Nami tends to fight, with the notable exception of Baroque Works (half its Officer Agents are female, although most of the Mooks are male), and all of Amazon Lily is female.
While half of the Soul Reaper lieutenants in Bleach are female, only two of the captains are. There is also only one female Espada and two former Espada, and the current one is the only one other than Stark to have female fraccion. Ichigo's team seems to be more balanced with a 3:2 guys:girls ratio
Though in the case of Starrk, Lilynette is actually his other half. When they were made into Arrancar, they separated into two bodies rather than just a body and a sword. Starrk specifically says, "We are the Primera [first] Espada".
Similarly with the Vizard. Though the number is almost equal with a 3:5 the Principle is still in effect since all three females are former Lieutenants while four of the five male members are former Captains.
Appleseed and Appleseed Ex Machina twist this trope by having the one and only female elite soldier, Deunan Knute, top every battle ranking. While she is the Smurfette with respect to numbers her role defies the trope's framework by fashioning her as The Hero as well as an uber-competent soldier who tops even her technologically-enhanced teammates (and foes), mechanical and biological alike. Note that the larger "team" including politicians and foot soldiers/pawns does feature many females, with politicians being almost exclusively female, e.g. Prime Minister Athena or Ambassador (and Deunan's friend) Hitomi. This is somehow handwaved by implying most politicians are bioroids for humanity's own good. Hyper-strong, but not unemotional, female leads are characteristic of Shirow Masamune's manga, from which both the Appleseed and Ghost in the Shell cinematic/TV works are derived. Actually, the female politician/male fighter "division of labor" seems reasonable even for real-world implementation.
If one looks closely during the opening action scene and the briefing room scenes, they can find the real smurfette. There's one other female member of E.S.W.A.T. (who is never named, never speaks, and sure as hell never does anything cool; that's Deunan's job).
In Axis Powers Hetalia, Hungary is the only female character who is regularly recurring. There are other females, but they have only been shown in a few strips or only on the artist's blog. However, considering the tone of the series and the fact that Hungary herself is a Yaoi Fangirl, this may be an example of a Cast Full of Pretty Boys.
Counter to the usual progression of such a circumstance, Hungary, Belarus, Ukraine, Lichtenstein, and Taiwan are all varying degrees of Ensemble Dark Horse. Vietnam, Belgium, and the African nations haven't gained such distinction, unfortunately. The fans' fondness of gender bending deserves mention, too.
Riza Hawkeye is the only woman in Roy Mustang's group in Fullmetal Alchemist. Somewhat justified in that there are fewer women in the military than there are men, and the reason she's in the group in the first place is because she's Mustang's aide, confidante, and bodyguard. She's The Chick only in the sense of being the sole female and dearly loved by her male counterparts; fact is, she's more badass than any of the other four subordinates. This may also be justified, as the country that the series mainly takes place in is an alternate-universe version of pre-World War II Germany, an era where seeing women in the military was a lot less common.
Olivier Mira Armstrong is the only known member of the general staff.
Among the homunculi, Lust is the only female (though Envy is genderless according to Word of God).
Heeello, BioMeat. One female lead the entire time (until part 3, which introduces a wise beyond her years 10-year-old), and the only one on the team without a specific role other than, you guessed it, moral support and maturity. Oh, and Cassandra Truth. Part 2 is especially glaring.
Presumably it's especially glaring because they're teenagers, which heightens the difference between girls and boys more than in elementary school. Bonus points for two of the boys, especially Shinko, having gotten pretty, and the fat one being less absurd-looking than before.
Revolutionary Girl Utena inverts this trope with the Black Rose Duelists (as opposed to the regular duelists chosen by Akio). Discounting the man manipulating them, Mikage, there are five girls that were chosen, and one boy, Mitsuru. Another boy, Tatsuya, was lured into becoming one but was rejected.
In Eyeshield 21, nearly every team has a female manager. While it IS understandable that there would a good number of female managers, as it's the only football-related position open to girls at most schools, the fact that there appear to be NO male managers for any team makes you wonder if it's a gender-specific position.
The only exception to the "manager" rule is the Teikoku Alexanders, whose token female is the quarterback.
Fist of the North Star only had one prominent female fighter in the manga and that was the village guardian Mamiya. In the Atomiswave fighting game, as well as in Ken's Rage, her fighting abilities are exaggerated for game purposes in order to match her against the Hokuto Shinken and Nanto Seiken masters, whereas in the manga she got overpowered by a mere nameless underling of Uighur.
In Death Note, Rem is the only female Shinigami to appear in the main story. The rest of the cast is predominantly male too, but this is justified somewhat by the fact that most of the characters are detectives or high-ranking businesspeople, which are predominantly male groups in real-life Japan.
This happens to the Kira Task Force in the Live Action Film, where Word of God states that she was added simply to make it so it wasn't an all male team like in the anime.
Also, Wammy's house apparently has only one female student, Linda, who appears very briefly in the manga and not at all in the anime seriesnote although she might be in the anime Compilation MovieDeath Note Relight 2: L's Successors; the character she's supposed to be is officially unnamed.
In Tantei Gakuen Q, Minami Megumi is the only female student in the Q-class, and her role is mostly limited to memorising and recollecting scenes with her photographic memory.
Possibly subverted with the A-class, because although Yukihira Sakurako is the only female until another female member joins in the group, she is the only one in the class who gets significant screen time, other than Plucky Comic Relief Saburomaru.
This trope is scaled up for Legend of Galactic Heroes. It's pretty conspicuous that there are only five notable female characters among a literal cast of HUNDREDS in a 110 episode saga, one of whom dies early on. The Alliance has an Action Girl and The Chick among its ranks, while the Empire has another Chick and the one woman who even comes close to the Magnificent Bastardry of the male characters. This is partly justified by the Empire's archaic social structures.
Tenchi Muyo! inverts this trope, with Tenchi being the only MALE main character. The rest of the main cast is female. The only other male characters (non-villain) that make regular appearances are Tenchi's father and grandfather.
Casca is the only woman in the Band of the Hawk from Berserk and mainly serves as Griffith's Number Two. She's quite respected by pretty much the entire band, at least some of whom refer to her as "anego" (sister). In time, she becomes the Love Interest of Guts. When the Eclipse goes down, she becomes the victim of a horrific Break the Cutie ordeal, culminating in her rape at the hands of Femto right in front of Guts. Two years after the horror, she and Guts form the core of a new group of True Companions later on, which is fairly evenly split between four guys (Guts, Serpico, Isidro and Puck) and four girls (herself, Farnese, Schierke and Evarella), but because of her traumatized post-Eclipse state, she's not the combatant that she used to be. It's also interesting to add that despite the introduction of other seemingly capable female warriors, Casca remains the series' only legit Action Girl.
JoJo's Bizarre Adventure is severely lacking in the female department until Part 6. Most of the women up to that point are either secondary characters or love interests with no real role in the story, and almost all the antagonists are men as well.
Averted in Part 6, with Jolyne Kujo as protagonist with two of her closest allies being women, and at least a couple of female antagonists.
Sailor Moon inverts this, Tuxedo Mask and Artemis being the only male (non-villain) primary character.
Toriko is very guilty of this. Rin is the only woman fighter of the main cast, and seems to be in a more supporting role anyway. Tina, a noncombatant, is somewhat more prominently featured than Rin, but in a World of Badass she sits in the realm of normal, Intrepid Reporter though she is.
Done kind of oddly in K: Each of the three main groups has exactly one female in them, but they're all fairly important, and of the unaffiliated characters, Kukuri gets by far the most screentime, and she's quite female. The end result is mostly the impression that the character designer didn't want to draw girls if they didn't have to.
Subverted with the Magical GirlPretty Cure franchise. Despite that all main characters are female, there are only a few females on the villain side. Every villain organization has maximal two females (per season), but they are never seen together because the second female is always introduced after the first one has died (with the exceptions of Yes! Pretty Cure 5 GO!GO!, Heartcatch Pretty Cure and Doki Doki Pretty Cure where the respective second female doesn't replace the former one because one of them is The Dragon). The seasons who have more than two females are Futari Wa Pretty Cure Splash Star and Smile Pretty Cure, however, the former has a pair of twins and they underwent a Heel-Face Turn before the third female shows up, making her the only female. And the latter series have a group of Psycho Rangers who appear for only one episode (actually, two - they appear in the end of an episode and are killed in the next one), so they can't really count as members of the villain organization, especially, there are just created by The Dragon, so they are actually more weapons than actual individual characters.
Not only that, every young female villain will undergo a Heel-Face Turn, reducing the number of female villains anyway. Suite Pretty Cure ♪ got it worst, since the only female villain joined the good side and no other female villain appeared in the show.
You think that the female villains are the important ones. Wrong! There are only five females of 16 Dragons in the franchise, yet. Yes, the other 11 Dragons are all male. Those said five females are Anacondy, Northa, Dark Precure, Siren and Regina. However, Northa and Dark Precure share The Dragon role with another male villain, respectively, and Siren is replaced by three males.
In the Lupin III franchise, Fujiko is the only recurring female character in the franchise, and even she was originally only a series of several one-shot characters, as a Shout-Out to James Bond.
While there are many female characters in the main and supporting cast of Log Horizon, there is only one female member (Marielle of the Crescent Moon Alliance) out of the 11 members in the Round Table Council, the player-run government of Akihabara. This is a result of the major guilds in Akihabara mostly having male guild masters.