Get Backers. There are a few women, but they are often shrugged off as "Ban's sister", "Ban's surrogate mom", "too old & too tall to be with" & "hologram tomboy". The rest of the cast is guys, some with very die-hard clingy relationships, & Akabane who only hits on a couple of guys while showing no interest in Hevn.
All Gundam series gets this, even the ones where the male characters are paired with (in Kira Yamato's case, actually have sex with) women. Especially Gundam Wing, in complete defiance of the show's 1-to-1 gender parity and about half those man/woman pairs being Official Couples or extremely close to it. Rarely this also applies to the women, usually by authors too kind-hearted to give them the usual treatment. This isn't helped by the director supposedly saying "I can't write boy-girl romances" (he actually said he couldn't write romance period) in an interview.
Hunter × Hunter. Many of the boys are pretty, friendships range from overprotective obsessed friend to acts-like-an-old-married-couple, there's a pedophile, very few women, & lots of fanservice pandering in the live musicals.
Jojos Bizarre Adventure gets a ton of this. Even without the at-times hilariously unsubtle Ho Yay (or Les Yay in the case of part 6), the huge imbalance in the number of male vs. female characters and the lack of romance in general makes it inevitable.
K-On!, as there just aren't many other options, along with Tsumugi being a Yuri Fangirl.
Monster. Never mind that Tenma was engaged to a female. Nevermind that Grimmer had a wife and a son. Nevermind that Runge has a daughter. Nevermind that none of them, in any possible light, look remotely bishonen (except for Johan)
Every senshi ever in Sailor Moon has been paired with every other in at least one story, with poor Mamoru often getting the short end of the stick.
Saint Seiya. There is no limit to the gay pairings in that one, since, well, about 95% of the characters are guys, and about 90% of them look effeminate in the manga. note e.g Camus' has prominent eyelashes and what looks like nail-polish & lipstick Never mind all the Bronzies are half-brothers. Everything's possible, even twincest with characters like Kanon and Saga who are hugely popular. The anime added its fair share of fuel to the fire by boosting the androgyny of characters like Lizard Misty and Aphrodite Pisces several levels, and by adding gratuitous instances of male fanservice.note Everyone agrees that Saga took way too many baths in a ridiculously short amount of time! And then there's the infamous Ep. 59 at Libra Temple, featuring the most Ho Yay overloaded scene on the whole Anime.
Weiß Kreuz was one the bastion of all shonen-ai fandom, with an extensive male cast (at least 8) with which to form manycrack pairings.
Descendants of Darkness. You can't throw a rock in that fandom without hitting a slash fic, and given that there are only three or four female characters that play a somewhat bigger role and/or appear more than once, shippers don't have much of a choice.
The Idolmaster to the point where some fans were enraged that a male was put into the show as the producer. Being the only male in an otherwise Improbably Female Cast however means he can still be largely ignored.
Slam Dunk: Never mind that the protagonist starts playing basketball to impress a girl, 99% of fanfics and fanart for the series is slash.
Sukisho: there are no women until the last episode. And that turns out to be a drag queen
Naruto: Statistically, at least one of the male characters in the cast has to be straight, but judging by the amount of yaoi fanfictions out there you wouldn't know it.
Beyblade. Because of it's Cast Full of Pretty Boys, fanfiction is about 90% yaoi. It can be pretty ridiculous but is unsurprising when there are 50+ characters and 9 prominent females, plus the mothers of two characters, a teacher & a minor character who was never seen after season 1.
The Marvel Cinematic Universe is chock full of this, the most popular pairings being Tony/Steve, Tony/Bruce, Clint/Coulson (despite them having only one onscreen interaction), and Loki and Tony usually end up banging everyone. However, like the Merlin example below, it is a rather peaceful multi-ship fandom, if only because Pepperony is adorable, Clintasha is popular and Peggy/Steve is cute, tragic and confined to the past.
Harry Potter fandom isn't this trope in general, but is large enough that enormous subsections exist that embrace this trope wholeheartedly.
That also goes for The Silmarillion. Again, there are many more male characters... oh, many are supposed to be married, but they're such a footnote often enough not even their name of the spouse is given.
About half the fanfics of the Jeeves and Wooster stories only feature Jeeves and Bertie anyway...
Blake's 7. One of the most-slashed shows ever, mostly because the show deliberately avoids making the characters' motivations 100% clear, so you never know what they're thinking and who they are really attracted to. Blake/Avon is the most charged, but it was an early femmeslash pioneer with Cally and Jenna.
The Daily Show. It doesn't hurt that Jon has described it as "the gayest show on television".
The Star Trek: The Original Series fandom are the ones who created slash as a concept in the first place, the ENTIRE main cast has been slashed together, no matter how weird the pairings have to be in order to Tie Up Romantic Loose Ends. The two main female characters, Uhura and Chapel, are shipped together just to even things out.
Happens more and more often in the Power Rangers fandom, but Het is Ew only comprises about half the fandom's opinion, so there's still a wide range of fic.
Merlin, due to the insane amounts of subtext in the show between almost every character, which also results in this being one of the most peaceful conflicting-ship fandoms out there.
iCarly has fics where everyone comes out as either outright gay or bisexual. Apart from the ever-popular Sam and Carly, Spencer often tells the girls that he is bisexual, usually with his best friend Socko, Wendy is often made gay so one of the girls can go out with her as part of the story's drama, Freddie comes out and admits he has a crush on Spencer, as well as admitting his crush on Carly is overcompensating to look normal.
Victorious can have this done, so that Jade can be hooked up with either Cat or Tori, whilst Beck and Robbie give in to their obvious UST and Trina just goes both ways because she's crazy like that and it lets Cat hook up with her if Tori ends up with Jade. Weirdly, Andre often gets left as the sole straight character.
Frequently the case in Glee fanfiction. This is helped by the fact that the show has numerous canon gay and bisexual charactersnote Kurt, Blaine, Santana, Brittany, Karofsky, Sebastian and Sandy, yet in fanfic even the canon straight characters are often shipped in same-sex pairings. For example, one of the most popular couples in the fandom is Rachel/Quinn, both of whom have only shown interest in boys on the show. By contrast, the gay characters are rarely shipped with opposite-sex characters once their sexuality is established on-screen, especially those who've had AnviliciousComing-Out Storylines like Kurt and Santana.
Sherlock. Excluding resident Jerkass duo Anderson and Donovan, if you know nothing about the series and look at blog sites like tumblr, you will probably assume the canon pairings for are John and Sherlock, Mycroft and Lestrade, Molly and Irene (both of whom vy for Sherlock's affections, so pair 'em off to get rid of them), and Moriarty and Sebastian Moran. It can be inferred the only reason Anderson and Donovan aren't paired off with people of the same sex within the fanbase is because there is no one left to pair them with AND nobody likes them. The only other heterosexual relationship that is even close to accepted is Molly/Lestrade.
Quite frequent in the Highlander fandom, and somewhat with the films too. It's probably kind of expected when most of the characters have lived for hundreds or thousands of years and writers feel they had a lot of time to experiment.
Ridiculously easy to do, what with all these big oiled-up hard bodies in very few clothes rolling around together in compromising situations, and probably something like a 10:1 ratio of men to women.
Half the cast of Rent is canonically gay anyway... and getting rid of Mimi to pair Roger up with Mark is more common than one might think.
Kingdom Hearts. In the fandom's eyes, there are practically no women or Disney characters, just Sora, Riku, Terra, Ven, Vanitas, 12 members of Organization XIII, Cloud, Leon and Sephiroth. If they're recognized, the girls are often shoehorned into being with each other anyway.
Mega Man and its other series have a cast that is mostly 99% male, making this inevitable. This is most certainly not assisted by the works of Hyadain for Mega Man 2, in which virtually every Robot Master is gay for Rock. Crash! Let's do it, indeed.
Much like the anime, the Pokémon game fics often pull this. The lead male and the (male) rival are very commonly paired off, with the lead female- when she does appear- being paired off with another female (for instance, Hilda and Bianca).
Tales of Vesperia has two really, really, obvious queer couples - Fluri and Ristelle - with buckets of subtext between them. Both pairings are extremely popular, and so it's not uncommon to have one pair play Beta Couple to the other in fanfic.
Fans of comics in The Walkyverse have a saying: "A character is assumed to be gay unless proven otherwise. And even then, it's suspect". It's mostly a joke... mostly.
For Eternity, a web remake of Rainbow Brite, has all the Color Kids (as well as its versions of Rainbow Brite, Stormy, etc) as male. Considering that the only females in that universe are childlike temple guardians or the four mother Goddesses, this is justified.
Most of the protagonists in RWBY are female, therefore most people who want to write shipfic will probably resort to this. There are het pairings that are widely accepted, like Pyrrha/Jaune and Nora/Ren, but only because those are pretty much canon. Unlike other examples of this trope, however, the full cast is fairly equal, with (by count of the characters page) a 13:12 ratio.
The Penguins of Madagascar uses this in canon and fanfiction. All the penguins have ambiguously gay moments, and we're still not sure if one or more of them is female. Meanwhile King Julien is almost certainly Bi the Way. Short of transferring OC female penguins, or going with Anybody/Marlene, gay is your only choice.
Metalocalypse, with its nearly all-male recurring cast, is ripe for this trope. While all of Dethklok does show interest in women (specifically, ladies), and Skwisgaar and Nathan are shown in bed with a few, all of the notable women they date look like the other band members. Combine that with the mountains of gay innuendo and the band's True Companions status, it isn't necessarily a matter of Everyone Is Gay as much as No One Is Straight. The creators are fully aware of it, too, with an entire episode devoted to a Dethklok fan-convention that cheerfully featured notable works of homos-erotic fan art produced by the fandom, and Murderface (the least popular band member and the one most likely to be canonically attracted to dudes) attempts plastic surgery so that fangirls will write more slash about him.
South Park, probably because there are so few important girl characters other than Wendy and Bebe. This despite how every one of the boys (including Butters and Cartman) have shown attraction to woman, many (including Butters) have stated that they're straight, and Stan had an off and on relationship with Wendy.
Transformers, for all of your CLANG CLANG CLANG action. Granted, giant alien robots are technically sexless, and the few female gendered Transformers are heavily outnumbered by the male gendered ones.
When the My Little Pony fandom isn't shipping the ponies with OCs or genderswapping the characters, they ship them with each other, and inevitably this trope is the result. The Improbably Female Cast in all series certainly helps, with G3 lacking any male characters aside from Spike.
In the Bad Future that is in an episode of Drawn Together, everyone is gay, by law. Future Spanky hated it so much that they created a super-hetero terminator to go back in time and kill Xander (because he's the one that creates the gay future).
Cabin Pressure. With a core cast consisting of three men and one older woman (who is moreover the mother of one of the men), what else are frustrated fan fic authors to do?
According to the comments sections of any given celebrity gossip blog, every attractive male celebrity is gay. No exceptions. If he has a girlfriend, she's The Beard. If he's seen in the company of another male more than once, this other man is his secret lover. If he marries a woman and gets her pregnant several times, it's a calculated move to protect his career by appearing heteronormative (which gives us the bonus Unfortunate Implications that all famous closeted homosexual men are perfectly happy to callously use other human beings, even their own children, for material gain). If he has stated on the record that he is actually bisexual, he defaults to gay because male bisexuality doesn't exist. If you point out that there is nothing beyond unfounded gossip to indicate his sexual orientation one way or the other, you are automatically a fat, ugly fangirl who is deluding herself and the sole reason gays are terrified to come out of the closet. Not surprisingly, no one ever questions the sexuality of, say, Steve Buscemi, Ernest Borgnine or any other male performer who is not conventionally attractive.