Gundam Wing has a primary cast of seven men (Heero, Duo, Trowa, Quatre, Wu Fei, Zechs, and Treize), and seven women (Relena, Hilde, Catherine, Dorothy, Sally, Noin, and Lady Une). Each of these characters also has a close relationship or strong bond with someone on the opposite sex list, making up the most common (non-gay) fan pairings; some of them are even Official Couples.
Bakuganused to have this, with three girls and three boys in the first season. Since then, it's been hit by the Smurfette Principlehard.
Princess Tutu has two guys (Fakir and Mytho) and two girls (Duck/Tutu and Rue/Kraehe). Bonus points for having one boy and one girl each as the protagonists/antagonists at any given time.
The Wheel of Time, to a certain degree, follows this by having a trio of males and a trio of females as the main characters, though it is rare that all six are in the same place at once or even directly communicating with each other.
The Mediochre Q Seth Series, if you only count the main four: Mediochre and Joseph are male, Dhampinella and Charlotte are female. If you include fringe members of the group who join them occasionally on adventures, it still sort-of works in the first book, because you can interpret Danny as being balanced out by Desra, the female mouse. Otherwise, it tends to fall apart quickly once you start including Rowan, Melz or Queen MAB.
Harry Potter: Although most of the series stars the central trio of Harry, Ron and Hermione we do get a temporary Gender Equal Ensemble when they're joined by Ginny, Luna and Neville for the climax of Order of the Phoenix.
Also the founders of Hogwarts consisted of two wizards (Gryffindor and Slytherin) and two witches (Ravenclaw and Hufflepuff) whilst the modern-day heads of houses are Professors McGonagall and Sprout (female) and Snape and Flitwick (male).
The first few of Jim Butcher's Codex Alera books have a gender-equal number of point of view characters. They start with Amara and Isana (female) and Tavi and Fidelias (male). The balance is preserved in the third book when Fidelias disappears and is replaced by Ehren, but is ultimately upset in the fourth book when Fidelias returns.
Also from Jim Butcher, the The Dresden Files book Changes has the initial group that goes off Storming the Castle at the climax: four men (Harry, Thomas, Sanya, Martin), four women (Murphy, Molly, Susan, Lea), and a dog (Mouse).
Up until the story The Nightmare Man at the beginning of series 4, The Sarah Jane Adventures' team consisted of two boys (Luke and Clyde), and two girls (Maria and Sarah Jane, later Rani and Sarah Jane).
When there are four people in the TARDIS on Doctor Who (something that's usually avoided because of how hard it is for the writers to find something for all those characters to do) the numbers tend to fall out like this.
Also, it's very common for the male Doctor to have a female Only Friend travelling with him.
Friends has three boys (Ross, Chandler and Joey) and three girls (Monica, Rachel and Phoebe).
Happy Endings: Three boys (Dave, Max, Brad), Three girls (Jane, Alex, Penny).
The Beverly Hillbillies - The titular family has two males (Jed and Jethro) and two females (Granny and Elly). Additional regular characters include two males (Milburn and Sonny Drysdale) and two females (Margaret Drysdale and Jane Hathaway).
The Brady Bunch - Not counting the housekeeper, the titular family consists of one father with three boys and one mother with three daughters.
The Addams Family - The immediate family consists of one father (Gomez), one son (Pugsley), one mother (Morticia) and one daughter (Wednesday). Extended family includes Uncle Fester and Grandmama.
Though it gets unbalanced if you count Lurch in.
iCarly: Sam and Carly are the women, Spencer and Freddie are the men.
If you consider Freddie's Mom as part of the main cast then it is uneven until Gibby becomes part of the main cast.
The Nanny - The Sheffield household has three males (Maxwell and Brighton Sheffield, Niles the butler) and three females (Fran Fine, Maggie and Gracie Sheffield).
Coupling - Three boys (Steve, Patrick and Jeff) and three girls (Sally, Susan and Jane). This was enough to get it described constantly as the Transatlantic Equivalent of Friends, when it wasn't much like it at all.
Though the group's composition is constantly in flux (often as a plot point), the titular Glee club of Glee spends most of it's time in an even 6/6 split between the boys and girls for season 1, and hovers around that number for most of season 2 as well.
The four main characters in Merlin are two boys (Arthur and Merlin) and two girls (Guinevere and Morgana). May not count for some considering the boys dominate most of the screentime, to the point where the girls are sometimes completely absent for certain episodes.
Final Fantasy VIII - The main party consists of three guys (Squall, Zell, Irvine) and three girls (Rinoa, Quistis, Selphie).
Possibly Final Fantasy IX if Quina is considered female. Four dudes (Zidane, Vivi, Steiner, Amarant) and four girls (Garnet, Freya, Eiko, Quina).
Final Fantasy XII - three males (Vaan, Balthier, Basch) and three females (Ashe, Fran, Penelo) make up the main party, although the group is occasionally joined by "guests" (important NPCs who take the unused fourth spot in a traveling party, all male).
Final Fantasy XIII - 3 main females (Vanille, Lightning and Fang) and 3 main males (Sazh, Snow and Hope).
Final Fantasy Type-0 - 7 main females (Rem, Deuce, Cater, Cinque, Sice, Seven and Queen) and 7 main males (Machina, Ace, Trey, Eight, Nine, Jack and King)
Pilotwings 64: Three male pilots (Lark, Goose, Hawk) and three female pilots (Kiwi, Ibis, Robin).
Dragon Age: Origins has four female Companions (Morrigan, Leliana, Wynne, and Shale) and four male (Alistair who is optionally replaced by Teyrn Loghain, Sten, Zevran, and Oghren). And a (male) dog. However, you don't have to recruit all of them and depending on whether you view the Warden as a ensemble member, the balance can be tipped to either side.
Mass Effect 1 had three female squad members (Ashley, Tali, Liara) and three males (Kaidan, Garrus, and Wrex), though Kaidan and Ashley become Mutually Exclusive Party Members after a certain mission. Mass Effect 2 leans slightly towards the male side, even with DLC, owing to the fact that Legion technically has no gender.
If you have the full party in Mass Effect 3, then you can have Garrus/James/Kaidan as your male squadmates and Liara/Tali/ EDI as your female squadmates. There is also a male DLC character called Javik who can tip the balance. However, he can also restore it, depending on how you see it, with males as Garrus/James/Javik and females as Liara/Tali/Ashley, with EDI as genderless.
In the first, with a female Player Character, there are four males (Carth, Zaalbar, Canderous, and Jolee) and four females (the Player Character, Mission, Bastila, and Juhani).
In the second, if the player character is light sided on Nar Shaddaa (and thus gets Mira instead of Hanharr), the party again has four males (Atton, Bao-Dur, Mandalore, and Disciple or the Exile) and four females (Kreia, Mira, Visas, and Handmaiden or the Exile).
Tales of Phantasia has Cress, Chester and Claus on the male side of the team while Mint, Arche and Suzu are on the female side, with Suzu being only recruitable in the remakes (and even then, she's optional).
Homestuck features eight boys (John, Dave, Karkat, Tavros, Sollux, Gamzee, Equius and Eridan) and eight girls (Rose, Jade, Terezi, Vriska, Kanaya, Aradia, Feferi and Nepeta). This even applies to large portions of the ensemble cast: the human session's exiles consist of two male Dersites (WV and AR) and two female Prospitians (PM and WQ), although the White King - a male Prospitian - briefly joined them, unbalancing the gender ratio. For about ten seconds before Jack Noir chopped his head off. The guardians fit if you treat Nanna as John's guardian instead of Dad Egbert. The trend is continued in the post scratch world with three males (Jake, Dirk, and uu) and three females (Jane, Roxy, and UU).
The regular contestants of Total Drama are split amongst eleven boys and eleven girls.
"The Incredibles" - two males (Mr. Incredible and Dash) and two females (Elastigirl and Violet). Technically, Jack-Jack unbalances this but he's not in most of the movie so it counts. If you include non-primary characters you have: Jack-Jack, Frozone, and Syndrome as well as Edna, Mirage, and Kari.
Scooby-Doo: Two boys (Fred and Shaggy), two girls (Daphne and Velma) and one dog (Scooby Doo).