There are several men on Martian Successor Nadesico, but only one, Jun Aoi, who is a regular member of the bridge crew (as opposed to a civilian who hangs out on the bridge giving Expo Speak or looking ominous). Akito's also the only male member of the kitchen staff and, for about a third of the series, the only male pilot - however, being the male lead, he doesn't really fit this trope.
Kyoutaro from Saki. He's the only guy in the Mahjong Club and, from what it seems, the only teenage male in the entire series. He's treated more like Yuki's errand boy, if anything.
Azumanga Daioh's own Kimura-sensei. There's also a semi-recurring classmate known by the fandom as TOD (That One Dude), whose biggest moment was to have his bike stolen by Yukari at the very beginning.
Makoto from Amanchu!, being Ai's hapless twin brother.
Komachi from Chu-Bra. Thanks to his big mouth, he's the only guy in the Underwear Appreciation Society, and Nayu and her friends are clearly more interested in debating which type of panties fit them best than paying much attention to Komachi.
Although he's the main character, Shinkuro of Kure-nai is also the only heroic recurring male character. All of the other major characters are female, of varying ages.
Kada is The One Guy from the Koihime†Musou anime. He shows up in a handful episodes during the second and third season and is the only character that is both heroic and male in the series. All other males are villains, mooks, or just not very good at fighting.
Akira in Ai Ore! Love Me! is the only boy in an otherwise all-girls band. Ironically, he's the one with the most feminine looks.
In Saki, Kyoutarou is the only male member of the Kiyosumi team, since all their other rivals in the mahjong tournament are all-girls schools. Unfortunately, since he's by far the weakest player on the team and the competition is only for girls, he can't play with his teammates and serves as errand boy.
Chase Stein of Runaways was the only boy in the group for a short time. Non-powered (after he lost the fistigons); drove the Leapfrog; dated Gert, the girl with the dinosaur.
Hawk is the only guy in the 2010 relaunch of the historically all-female Birds of Prey. Obviously, it's because Hawk and Dove are a package deal and his bird motif certainly fits in otherwise.
In the New 52Birds of Prey series, Condor joins the originally all-female team in issue 16.
Scott Lang, the second Ant-Man, is the only male chosen by the Fantastic Four to replace them in what's supposed to be a four minute absence from Earth. He joins She-Hulk, Medusa and Johnny Storm's current girlfriend Darla Deering a.k.a. Ms Thing.
Takara in Rising X Rydeen is the only boy and leader of his superpowered team. This is because the higher-ups for the organization he works for are a bunch of dirty old men. They wanted an all female team, but, for reason's unexplained, Takara is part of their grand plan so they reluctantly added him.
In Boys Und Sensha-do, there are about 16 new male OCs. A fair portion of them join pre-existing teams as the sole male member.
Buffy the Vampire Slayer played this to the hilt, with the Scooby Gang's makeup became increasingly female starting with Season 5. After Spike left near the end of Season 6, Xander was temporarily the only male Scooby in Sunnydale (until Giles returned in the last episode). The male demographic increased in Season 7 with the return of Spike, but the arrival of the Potentials permanently shifted things towards the female side.
Xander lampshades this in one episode when he says that the Magic Box is like "NORAD, and we're at DEFCON 1" and the room full of women just stare back at him, prompting him to sigh "I so need male friends."
Continued in Buffy Season 8, at which point Xander is pretty much the only guy in the gang — which now includes a whole bunch more women. (Plus Andrew and, albeit temporarily, Dracula of all people.)
Army Wives has four army wives and one army husband. But to be fair, the military husbands and military wife are prominent characters as well, so it feels more like an even gender balance.
In Pushing Daisies, out of the main six characters, only two are male (although two of the women are missing from a fair few episodes).
Henry Rush in the 1980s sitcom Too Close for Comfort. Subverted in the second season when Jim J. Bullock (Monroe Ficus) was promoted to series regular status.
Allen Anderson of the regular kids on Punky Brewster. He left at the start of season 3 (and boy, did it break Punky's heart).
In New Girl Schmidt is this at his job. Rather than a dream job for him, though, his work is dismissed, he's sexually harassed by his superiors, and treated as being inferior to all the women at his job. Not played for laughs all the time.
Noob shows the Girl-Show Ghetto TV channel for which Omega Zell works to have many female employees in the comic and has him complain about being surrounded by many women at work in the webseries. The novel reveals he really is the only male employee of the place (long story short, the boss thought his real life Gender-Blender Name would somehow make him fit in perfectly).
WWE's "Santina Marella" during the "Miss Wrestlemania 25" match.
When Vickie Guerrero formed an alliance with Lay Cool, her boyfriend Dolph Ziggler became the one guy of the pseudo stable.
During WWE's "Attitude Era", the stable Pretty Mean Sisters (Jacqueline, Terri Runnels, and Ryan Shamrock) had "Meat" (aka Sean Stasiak), who was passive and obedient to all three, and heavily implied to be their sex slave.
Touhou has such a powerful Improbably Female Cast that even these guys are marginalised. The only known males in Gensoukyou aside from briefly-mentioned background characters are Genji (Reimu's former assistant, is a flying turtle, hasn't been seen since the PC-98 games), Unzan (Ichirin's assistant, doesn't have a single line, is an angry pink cloud, and is so manly despite all this he's an Ensemble Darkhorse), and Rinnosuke (only appears in one Expanded Universe manga). Word of God is that there are plenty of males, it's just that most of them don't fight so the player doesn't see them.
In Final Fantasy V, Bartz becomes The One Guy of the party when Galuf is replaced by Krile. Humorously enough, it was originally a case of The Smurfette Principle, as the party is made up of four members, with Lenna being the only one openly female, as the fourth member, Faris, tried to masquerade as a man due to being raised by pirates and becoming the captain.
When Electric Wonderland began, the roster of main characters consisted of three women and one male: NJ. Two more males, Torro and Parker, joined in the second comic, but Parker got swiftly Put on a Bus. Also, Torro rarely contributes anything worthwhile to the characters' adventures, for being Too Dumb to Live. This results in NJ still holding this title most of the time.
Whateley Universe has Lancer, the only guy in Team Kimba, however there are plenty of reoccuring male characters outside Team Kimba. Also somewhat subverted in that Lancer used to be female.
Phase is another guy on Team Kimba, but most people wouldn't know that looking at him, due to his mutation turning him into an intersexed hot chick physically. He gets almost as much pronoun confusion as the J-Team out of it.
She-Ra: Princess of Power featured Archer Archetype and Master of Illusion Bow. Bow is one of the only recurring non-villain male character, besides He-Man's frequent cameos. The vast majority of enslaved townspeople the Rebellion rescues are male. The Sea Hawk and his crew. And there's Kowl and Light Hope; none of them human and none of them even remotely likely to be Love Interest to anyone, but both of them male and both of them major enough characters to be explicitly mentioned in the opening.
My Little Pony: Friendship Is Magic has Spike again, although in Season 2 Big Macintosh was promoted to share this slot with Spike, usually trading off. If one is missing chances are the other one is hanging around.