In Water Margin, there are 108 heroes of Liangshan Marsh, divided into 36 'heavenly heroes' and 72 'earthly heroes'. Only 3 of the earthly heroes are female, and none of the heavenly heroes are. Additionally, only one of the women survives the novel.
Leah Clearwater in the Twilight series is the sole female werewolf not only in her pack, but in HISTORY.
The Hitchhikers Guide To The Galaxy series contained only one major female character for the first three books. Douglas Adams explained in an interview that he wasn't comfortable writing female characters because he didn't understand women. He made up for it in the third book by allowing Trillian (instead of Arthur, as he had originally planned) to make the deductive leaps that narrowly prevent a galaxy-wide war. Books four and five added Fenchurch and Random, respectively.
In Orson Scott Card's Enders Game, Petra is the only girl ever mentioned at the Battle School; when Ender is first recruited, it is mentioned that girls rarely pass the tests to get in. However, Ender's sister Valentine proves to be an important character. Later books in the series introduce more major female characters.
Eventually, Petra winds up first a kinda-Satellite Love Interest and then a babymomma. To something like eight kids. And settles down with Peter, of all people, since Bean had to go away into space with the mutant babies and you can't have a woman alone. (Unless she's a nun. The nun was cool.) Be fruitful and multiply indeed.
Tamora Pierce has stated she writes stories with female leads precisely because of this. At the time she was starting the Circle of Magic series, she saw an article that mentioned that 75% of recently published fantasy books had male heroes, so she inverted the figure by having three girls and one boy as the main characters (a male character with stereotypically "girlie" plant-based magic at that).
The teachers were two men and two women, though, and Sandry also had Duke Vedris.
However, Pierce does have a roughly equal number of male and female secondary characters in almost all the books.
And sometimes they overshadow her girls, especially when she gets to the romance stage. Still, she does all right. In the Trickster books even the Love Interest didn't hold a candle to Ally for character-dominance. Of course, the relationship had a really odd progression. Starting with the fact that he's a crow.
The Discworld novels includes a Violent Glaswegian version of The Smurfs, called the Nac Mac Feegle, or Pictsies. The Nac Mac Feegle, though humanoid, can be considered an extreme case of Insect Gender Bender, in which the gender of the 'worker bees' is reversed. Their hundreds-to-one sex ratio is explained in that the females are rarely born, but are "Queen Bees" (Keldas) who rule over their sprawling, brawling sons, brothers-in-law, and husband. Keldas may, when fully grown, be larger than the males of the species (Big Aggie of the Long Lake Clan, for example).
The Discworld Watch books feature only two non-dwarf female Watchmen. They're even Twofer Token Minorities (one is a werewolf, the other a vampire). There ARE other female Watch Officers- a Constable Jolson may have been vaguely referred to as 'she'- but they don't get screen time.
Leave us not forget Corporal Cheeri Littlebottom, the unfortunately-named one-dwarf forensics department of the Watch. Of course, it's not obvious that she is a she until the end of the book in which she's introduced, but that's par for the course for Discworld dwarves. Littlebottom later starts a sort of feminist movement for female dwarves by making it obvious that she is female, which is apparently a serious taboo for dwarves.
The Lord of the Rings features very few women. The actual Fellowship is completely male, and the only female character to take an active role in the sprawling thousand-page plot is Éowyn. Galadriel is powerful and important, but mostly "offscreen". Lobelia Sackville-Baggins, Mrs. Maggott, Goldberry, Ioreth, Mrs. Cotton, and Rose Cotton are trivial. Arwen barely has a speaking part. Everyone else is male.
Tolkien does point out that her people have a tradition of warrior women. Peter Jackson's films are actually much better examples of the Smurfette principle than the books.
Tolkien also mentions that there is only one known dwarf woman in history - Fíli and Kíli's mother, Dís (who is briefly mentioned in The Hobbit and in the appendices to Lord of the Rings). Others certainly exist, but she is the only one who is named. Though it's also noted that on those occasions dwarf women travel, they are commonly mistaken for dwarf men by non-dwarves who can't tell the difference.
The Silmarillion has a few more female characters (such as Melian, Haleth, Lúthien), but they usually end up being defined by their relationship to male characters, who get much more page timenote Though Beren is as much defined by his relationship with Luthien as she is by her relationship with him.
Fate Zero has a bit of this with Saber, a Gender Bender version of a traditionally male character to start with and the only female amongst individual servants. It repeats again with the Assassins with one female and three males on the team.
From 72 demons featured in Ars Goetia, only Marchosias, Vepar, and Gremory are female. And that's only from their usual forms on manifestation (respectively: gryphon-winged, snake-tailed she-wolf; mermaid; camel-riding noblewoman); the text itself still uses male pronouns for all the demons. Marchosias, Vepar, and Gremory included.
The only female disciple of Aldur in Belgariad is Polgara. Well, also Poledra, but she's a Missing Mom most of the time. And these women are Belgarath's wife and daughter, so apparently to be a female member of the group you have to have a connection to a male member of the group. Although Poledra was called in her own right, and had been around for several centuries as a wolf before taking a human form and name and marrying Belgarath.
Isaac Asimov, until he married his second wife had issues with women due to relations with his beloved Smother. Susan Calvin was the shining exception in the 400+ books he wrote until he was old.
Of Mice and Men: There are a total of eleven characters mentioned in any capacity in the book. Two are women. One, Lennie's Aunt Clara, deceased, is never seen and is only a part of Lennie's background. The other, Curley's wife, doesn't get a name. And she dies anyway.
The Mythos also has Cthylla, who is the only "daughter" of Cthulhu's offspring.
A subtler version is at play in Zamyatin's We: everyone in the society is issued with an alphanumeric designation instead of a name, with one letter followed by several numbers. Men get consonants; women get vowels. Note the ratio.
Except in Russia, the ratio is about 2:1 - 10 vowels, 20 consonants, so it's not as extreme.
In Sharon Creech's The Wanderer, Sophie is the only girl among the surly crew of the titular sailboat, made up of her three uncles and two (male) cousins. And they didn't even want to take her in the first place. Their main reasoning was "wouldn't you rather stay at land, where you can take shower every day?".
Light And Dark The Awakening Of The Mageknight: For a long time Sabrina was the only prominent female character other than Danny's mom. When she left the group, she was promptly replaced by Briza. Also, there is precisely one female among the White Rock Academy Instructors.
There are several instances of the smurfette in Harry Potter:
The three main characters are two boys and one girl
Ginny is the token female in a family full of boys
Deconstructed in the first Artemis Fowl book when Holly Short flat out asks her commander if he is harder on her because she is a girl. Root says yes ... because she is the first female officer in Recon and therefore must set a good example.
Technically, A.L. Phillips's The Quest of the Unaligned counts as an example of this, but though there is only one girl in the main party, there is only one boy for the first half of the story and only two for the second half. So Justified in a rather meta way.
Mildly deconstructed in Mistborn: The Original Trilogy. The setting's criminal underworld is heavily male-dominated, and as a result heroine Vin- raised to be a thief by her thief half-brother- has been the only (or one of the only) girl or woman in any given situation for most of her life. This has a very visible influence on her personality.