Of the gang of playable characters in Borderlands, three are male and one is female, who are all with a fourth man driving the truck. The female is introduced as "The Siren," which is barely a gnat's whisker away from simply calling her "the token girl."
In Bully, each social clique has only a single female member versus about half a dozen male members.
Fatal Fury: The first game lacked any female fighters. In the second game, Fatal Fury 2, eight new fighters were introduced, including the first female fighter in the series; the kunoichi Mai Shiranui. By the third game, it's established that female characters are introduced every game, but due to rotating some of the female characters out of the games as well, it doesn't guarantee that a given work in the multimedia franchise will have more than one female.
The original version of Final Fantasy III stars the all-male Onion Knights; the remake for the DS makes one of them a girl.
Every single-player game since Final Fantasy IV has a rule to avert the Smurfette Principle. Exactly three female characters in the playable cast, regardless of the total cast size. This even extends to entries of small cast sizes, like Final Fantasy V (three women, two men) and Final Fantasy X-2 (an all-female party of three). Because later games have gravitated toward a total playable cast size of 6, Gender-Equal Ensemble is in effect.
For the longest time, Chica of the Five Nights at Freddy's fame is the only animatronic officially confirmed to be a female. The principle is averted as World adds another confirmed female (JJ) and Sister Location adds a number of new female animatronics.
The only women in the entirety of Half-Life are the black-clad assassins who never speak and only appear in two areas. Also, despite Black Mesa claiming to be an "equal-opportunity employer", all of its employees seen in the original are men, except for the holographic assistant in the tutorial. The cooperative expansion Half-Life: Decay for the PS2 fixed this by having you play as either Gina Cross (who apparently lent her voice and likeness to the holographic assistant) or Colette Green.
Halo 4 Spartan Ops: Fireteam Majestic begins with Tedra Grant (female) as part of the original Majestic line-up, along with Anthony, Carlo, Paul, and Gabriel (males). Naiya Ray is introduced in Halo: Escalation.
Kerbal Space Program added a fourth playable character quite late in the development process; originally the kerbals were a Single Gender Species. This can be seen as Invoking the Smurfette Principle because Valentina is a female clone of Jebediah, other than a slight stat difference (she's marginally smarter and more courageous), she's superfluous because the original 3 males already cover all 3 character classes (Pilot, Engineer, and Scientist). However, the game provides a method for the player to avert the Principle with an endless number of randomly-generated astronauts of either gender can be hired to adjust the crew's gender ratio as you choose.
Killer Instinct features eleven fighters. Initially, Black Orchid was the only female on the original cast of KI but when development started on season 2 of the 2013 game, it was revealed that Riptor is and always was a female, meaning the original KI actually had two female fighters.note Of course Riptor being a human-raptor hybrid meant there's still only one female in a group of ten humans.
While there are a small handful of important female NPCs, when it comes to the playable characters, the three main characters are all male, and there's only one female Guest-Star Party Member in each game; Ariel of The Little Mermaid in the first one, and Mulan of Mulan in KHII.
There's also Organization XIII. Out of thirteen members, there is only one female, that being Larxene. The creators originally planned on making Marluxia female as well, but changed their minds.
Left 4 Dead and its sequel justify their decision to use only three men and one woman as playable characters: The gene to be resistant to The Virus is recessive and carried on the x-chromosome. Women need two copies of the gene, while men only need one, explaining the genetically sound 3:1 ratio.
The Legend of Zelda: For a given game, the Zora characters have usually only one female among a sea of muscular-bodied males.
Mega Man (Classic): The villains use the following naming scheme — every Robot Master is called <word> Man. During Mega Man 9, one of the eight villains was Splash Woman, finally participating in the Smurffette Principle.
Despite being the flagship Action Girl of the video game world, Samus Aran of Metroid fame managed to become the Smurfette in her own series in Metroid Prime: Hunters. Six new bounty hunters were introduced, all of them male or ambiguously so. Metroid Prime 3: Corruption is more gender-balanced, as one of the three new hunters is another female.
Out of the dozens of characters in Modern Warfare, the only female character is your fellow Cobra pilot "Deadly" in the first game. Mostly justified by being a military game; while women are no longer barred from joining in a lot of places, real life militaries are still heavily male dominated.
Let's see, Mortal Kombat... For the first game, the creators realized they didn't have any female fighters in their roster, so they changed the character of male Kurtis Stryker into female Sonya Blade (Stryker would be re-added in the third game). This made her the only female out of 7 playable characters and 10 fighters overall. Later games have made sure to include additional female playable characters from the start.
Nezumi Man has Wave Nezumi, the only female boss of the eight.
In One Piece Mansion, Raspberry gets the descriptor of "The only female in Syndicate 5".
The original Japan-only version presents the Inverted Trope of many female characters and the only (confirmed) male character being Sanatos, the Big Bad.
The Western reskin, Tetris Attack plays the trope straight, with Naval Piranha being the only confirmed female character.
Most Resident Evil games avert this, but while Resident Evil has two major female characters, they are the sole female members of their respective STARS teams (Jill for Alpha team, Rebecca for Bravo team). Weirdly, in early games, there are almost never any female zombies (the first game only had male zombies, while the second and third games had only one female zombie model among a slew of male models); this is averted by the time Resident Evil 0 rolls around, and the Gamecube/Wii remake of RE1 added Lisa Trevor.
In Robopon, in the first game, Miss Amron is the only female Legend out of seven. (Kamat may or may not be a girl). This is averted with the Elite 8: All of its members are girls.
In Scribblenauts Unlimited, Maxwell has many, many siblings you can unlock and play as. All but one of them are brothers, and the one sister is the Damsel in Distress.
Sengoku Basara spinoff fighting only had Oichi as the only "true" playable female character of the sausage fighting fest. The rest of the girls are delegated to backup.
In the first Shin Megami Tensei, all of the Seraphim (Michael, Uriel, Raphael, and Gabriel) were presumably male, but the second game reveals Gabriel is a girl, and all subsequent SMT and Persona games featuring Gabriel retain this.
In the Sly Cooper games, there will often be one female villain per-game (the second game has two villains, one of whom is the Big Bad). The Cooper Gang itself started off as an all-male trio, then became a group of seven in the third game, with Penelope as the only female. In Thieves in Time, Penelope pulls a Face–Heel Turn, resulting in the Cooper Gang being all-male again.
Sonic the Hedgehog was never character-heavy in its early games, but no female character was even seen until Amy Rose, who looked like a little pink Sonic in a dress. More characters have been introduced as the cast has expanded, but the majority have been male. In Sonic Lost World, out of all members of the Deadly Six, only Zeena(the green one) is female.
Spyro the Dragon had no important female characters at first. Then along came Bianca and Elora, with the first being a sort of villain and the other just a love interest, then Sheila, a female kangaroo. Even in the Legend of Spyro series, Cynder is the only important female character, with no others present. Largely continues into Skylanders; out of 80 total Skylanders through 3 games, there are only 14 female characters. Only one of the 8 Giant Skylanders is female, none of the Swap Force Skylanders is female, and it wasn't until the third game that a female Fire Skylander was added. At least the Swap Force case has a reason due to the LEGO Body Parts mechanic; mixing males and females would be... awkward.
Starcraft had exactly one named female character: Sarah Kerrigan, who is betrayed but rapidly becomes the queen bitch of the universe as the Queen of the Zerg. The expansion set added the Protoss matriarch Raszagal (the only female Protoss for the next ten years). Starcraft II expands the universe a bit, including adding supporting female human characters, but with Raszagal dead, the role of "only female Protoss" is inherited by Executor Selendis, who will is the protagonist of the second expansion set. Starcraft: Ghost's main character was to be a female Ghost, not unlike Kerrigan.
The Star Fox games follow the principle. The original game, and its remake, Star Fox 64, featured an all male membership in the title team (bad jokes about Slippy's Ambiguous Gender notwithstanding) and only one female character period—sometime ally Katt, who assisted you in Zoness and Sector Z. It wasn't until Star Fox Assault that the team gained a permanent female member: Krystal from Star Fox Adventures. The unreleasedStar Fox 2, however, would have added two female characters to the roster - Genki Girl Fay and Action Girl Miyu. And in Command, there are a solid 4 females: Krystal, Kat, and newcomers Lucy (Peppy's daughter) and Amanda, Slippy's female love interest. There is even an all-girl mission. Unfortunately Star Fox Zero reboots the series, and Kat is back to being the only female in the Lylat System.
Both Star Wars: Battlefront I and II feature at least four factions and have as much as three female characters, the generic Rebel Sniper class (which is excluded in a few maps), Princess Leia, and Aayla Secura, the latter two both hero class characters limited to appear in as much as four maps (if you count Hero Assault). If you own the Xbox version there is Asajj Ventress hero character from the DLC.
The first iteration of Street Fighter II had only one female warrior out of twelve fighters, Chun-Li. (She is often called the First Lady of Fighting Games by fans, as she was the first female of the genre, period. One of Chun-Li's win quotes in Tatsunoko vs. Capcom, which has a roughly even male/female mix, makes fun of this: "I remember when I was the only girl on the roster.") This gradually changed through the course of the series with the introduction of Cammy in Super Street Fighter II; Rose, Sakura, R. Mika, Karin, Juni and Juli in the Street Fighter Alpha series; Ibuki, Elena, and Makoto in the Street Fighter III series; and Crimson Viper and Juri in the Street Fighter IV series.
The cast of crossover characters from Final Fight initially featured four characters, all male, but this changed with the addition of Maki (from Final Fight 2) in the portable versions of Alpha 3.
The Super Mario Bros. games' only recurring female character was Princess Peach, who was usually a Damsel in Distress. This changed as Princess Daisy and Birdo became full-fledged main characters and with the introductions of Toadette, a feminized Toad, and Rosalina, both of which were somewhat less stereotypical than Peach. The ratio still heavily favors males.
The first two Mario Party games had Peach as the sole playable female character. This was changed in Mario Party 3 when Daisy was added to the cast.
On the villain side, the first evil female was the single girl of the Koopalings, Wendy O. Koopa. Captain Syrup showed up later as Wario's nemesis, and some stage bosses were female (Naval Piranha). Lately the villainous ladies have become more numerous with Cackletta, the Shadow Queen, Princess Shroob and Elder Princess Shroob, Mimi, the Shadow Sirens, and Robirdo.
Out of 13 new characters in Super Smash Bros. Melee, three new females were introduced (Peach, Zelda and Nana). One of whom (Nana) teamed with a male character as the Ice Climbers. Super Smash Bros. Brawl didn't add any females to the cast, though it did make the gender of Samus and Sheik more visible.
The Wii U and 3DS iteration subvert this trope: There are more female characters then ever before, but due to the sheer cast size, they're still outnumbered by male characters. While Nana was removed, Sheik and Zero Suit Samus were made separate characters, the Wii Fit Trainer is female by default, there's the option to play as female Villagers, female Robin or Wendy, Miis can also be female (with the official artwork for the Mii Gunner being represented by a female Mii) and finally, Rosalina, Palutena and Lucina were added. That makes it roughly 13 female characters in all, bigger then the first game's entire roster. The final DLC characters introduced to Smash (female Corrin and Bayonetta, the Smash Ballot winner) increases that number to 15 out of 58 fighters, over a quarter.
Three crossovers which come to mind that have larger amounts of females than others are Super Puzzle Fighter II Turbo, Pocket Fighter/Super Gem Fighter Mini Mix, and Cross Edge.
Most Super Robot Wars games allow the player to choose between an equal number of male or female original characters. While this doesn't quite help the ratio among the licensed games, it makes for a more or less even mix among characters in the Original Generation series.
Team Fortress 2: The only obvious woman in the game is "The Administrator", aka the angry voice that screams at you during rounds. Admittedly, the Pyro may be female (or genderless, for all we know), and the comics also have the character Ms. Pauling, but if you look just at the game, it follows this trope.
Time Crisis series has one featured female among the multiple male casts per game in order:
1: Rachel Macpherson
2: Christy Ryan
3: Alicia Winston
4: Elizabeth Conway
5: Catherine Ricci
Crisis Zone: Mellisa Kessler
Torchlight has the same gender ratio as Diablo I (not surprising, considering the similarity between the two games and many of the same developers). Also like Diablo, the lone female happens to be the physical ranged damage dealer.
Several of the Ultima games have a less-than-favorable ratio. While the eight "Companions of the Avatar" had a 4:4 ratio, the females generally had worse stats. (By design in Katrina's case, as Shepherds by design aren't supposed to excel.) The trio of Iolo, Dupre and Shamino (all male) also kept gaining prominence over other characters as the game went on. The eighth and ninth games even disallowed playing as a female main character!
Warcraft: Orcs and Humans had a half-orc, half-human (who was later retconned into half-Draenei) girl, Garona Halforcen, present in one mission, but no-one else.
In Warcraft II, no generic humanoid units were female, and neither were any individual hero units until the Expansion PackBeyond The Dark Portal introduced a lot more of them, and exactly one was female: Alleria Windrunner. In a weirder example, exactly one building unit was basically a female character (whereas others were of course genderless): the Dragon Roost consisted mostly of Alexstrasza the Dragon Queen, chained down to act as an egg factory.
Out of all the 12 heroes available in the initial third Warcraft, only one is female (Priestess of the Moon). The expansion averts this by adding three more female heroes (Warden, Dark Ranger, and Naga Sea Witch).
The Orc gender balance was also acknowledged in World of Warcraft in that the orcs actually were sexist. Despite being every bit as aggressive and strong as the men, women were denied combat roles. Thrall changed that between WC3 and WoW. (Then again, if you look at the "old" clans on Draenor in the Warlords of Draenor expansion, most of them do have female warriors, though at least the Bleeding Hollow don't.)
Wild ARMs 1 and 3 both follow this trope. Each of the two games has one playable female character (teamed up with two or three males), though Cecilia and Virginia are each portrayed as the one calling the shots. Wild ARMs: Alter Code F, a remake of the first game, alleviated the gender issue by adding Calamity Jane and Ema to balance the cast (Zet, a guy, is also recruitable).
Wolfenstein 3D has one single female in both series, who is a boss that looks almost exactly like her brother and has a low voice.
Four main playable characters in The World Ends with You, and you can count how many of them are female on the single hand of a blind butcher.
Citrine is the only female URTV shown in the Xenosaga trilogy, even though she stated there are 8 others like her.
Many early computer games would let the players choose their gender (as well as, often, other attributes like name, race and age) at the start of the game (unless you were a Featureless Protagonist, of course). As the amount of assets (graphics, voice acting, and sometimes even onscreen actors) needed to portray player characters increased, many studios discreetly dumped this feature. Modern games that let you choose a gender offer varying amounts of plot and gameplay branching as a result of the choice.
Gate of Doom, known in Japan as Dark Seal, has three male heroes (Knight, Bard, Ninja) and one female (Wizard). The Wizard is a Hot Witch who shoots pillars of flame and wears a costume that hides one leg and exposes the other.
Gauntlet has three male (Warrior, Wizard, Elf), one female (Valkyrie). Sequel Gauntlet Legends averts this by changing the androgynous-looking elf to a female elven Archer. Dark Legacy falls back in when adding four more characters to the existing four: three male (Dwarf, Knight, Jester) and one female (Sorceress). As well, the breasts on all the women became about twice the size of their heads. Seven Sorrows then goes back to the original four characters. Get Medieval, a Spiritual Successor by Monolith Productions, kept a 2:2 ratio by turning the Wizard into a naughty sorceress whose every line was a Double Entendre. (Okay, some were even single ones...)
Both Left 4 Dead games have one female in a group of three males. In the sequel, the two groups meet so it's two girls with six guys. Most of the NPCs in the games are male, including the special infected until the Spitter and the female version of the Boomer were introduced in the sequel. The common infected, however, are both male and female.
On a related note, many other fighting games fall victim to the same problem, but not because they're drawing from other canons. It is rare to find more than a few female characters available to play out of an otherwise large collection. Generally, the female characters are also notably weaker than the male characters. This is parodied in VG Cats — here.