Gafinilan and Mertil. In the Animorphs series, they either have a very close and important friendship or the most well-written romance in the whole series. We don't get definitive evidence either way.
Archer's Goon: Torquil. Has a great love for theatrical outfits (eyeliner included), shopping, and disco dancers. This trope is even more true for the TV miniseries.
In the Aunt Dimity series, Grant and Charles aren't mentioned as gay, but they show all the signs. Their careers are in the art world, specifically in restoration, framing, and appraisals. On first moving to their cottage in Finch, they compete in the village flower show and win. They have a pair of small pet dogs named for artists. They're just as much the Gossipy Hens as any of their neighbours; they share a table with Lori at Sally Pyne's cafe to watch Amelia move into her cottage. The morning after their cottage is broken into in Aunt Dimity and the Village Witch, Charles is prostrate on a chaise and fortifying himself with alcohol, and Grant offers a drink to Lori before preparing one for himself.
Kristy Thomas. She loves sports, dislikes girly accoutrements such as dresses and makeup, and all her strongest emotional attachments are to female friends. She showed much less interest in boys than the other main characters and, despite having an on-off boyfriend (Bart), was never as serious about him as the other girls were about their boyfriends - then ultimately dumped him when she decided that something didn't feel right about the relationship. The Nostalgia Chick pointed out in her review of the 1995 movie that it features what can only be described as a Longing Look between Kristy and Claudia.
Abby Stevenson, who is also tomboyish and develops a very close friendship with Kristy late in the book series, may also fall into this category.
In the spin-off California Diaries series, Ducky counts as this trope. He has no romantic interest in his female friends and all but explicitly tells Sunny that he can't date her because she is a girl. In his last appearance in the series, he's seen buying a number of books by openly gay authors. A writer confirmed to a fan on Twitter that Ducky is gay; but the novels leave it open-ended.
Higgins from The Bloody Jack series although it's not so much ambiguous as heavily implied. Also, Mam'selle Claudelle day Bourbon in the second book. Her actions around Jacky are a bit suspect.
A romantic relationship between two men (Sebastian and Charles) plays fairly prominently into the plot of Brideshead Revisited, but because the book was published in 1945, the "true" nature of this relationship is never explicitly stated.
In Bumped, Harmony's husband from her failed Arranged Marriage, Ram, is implied to be gay. They were placed with each other because they both had issues (she ran away from her first marriage).
William Marsh in Darkness Visible. How ambiguous it is depends on whether or not the reader picks up on late-Victorian gay traits or not. For example: smoking thin white cigarettes, dressing flamboyantly and (implicitly) hanging about with Oscar Wilde...
The Discworld novel Unseen Academicals has Pepe. On the one hand he's very camp in his role as a fashionista. On the other hand, he's not like that at all when he isn't working. On the third hand, his "real" characterisation edges slightly towards Macho Camp. On yet another hand, he may be in relationship with someone who identifies as female, but on one more hand still she happens to have a huge beard and come from a culture where gender isn't considered important and many women identify as male. On the final hand, Word of God says "He's probably as gay as a tree full of monkeys, but you can never tell. Fandom has a few of them; they've reached a sexual equilibrium and you just don't ask questions."
Oreg from Dragon Bones has impeccable manners, taste in clothes and "feminine" hobbies. He is also very close to Ward, although that's in part due to the dark magic that eternally enslaves him to the wearer of a ring, which Ward happens to have inherited from his father.
The Doctor in the Eighth Doctor Adventures novel The Blue Angel. (It may be important to note it's in an Alternate Universe where he's a slightly abnormalhuman.) He's something of a Supreme Chef, and certainly a very dedicated cook (he panics about having overcooked the potatoes). He redecorates his house to relieve stress and listens to Bette Davis soundtracks. And Freud might find the fact that he's a Momma's Boy to be rather significant. His Heterosexual Life Partner, finding him outside in the snow fussing over the garden, puts his arm around his waist to lead him inside. Most interestingly, in the parts taking place in the normal continuity, he's referred to as a "fussy old confirmed bachelor", which is basically a euphemistic way of saying Camp Gay. The Other Wiki says this was a bit controversial, and Paul Magrs, the openly gay author of this book and some of the more idiosyncraticDoctor Who novels, has stated that he writes the Doctor as a middle-aged celibate gay man.
Hippolyte Swanson, the guardsman-turned-heroic dressmaker in K.P. Bath's Escape from Castle Cant.
Zil Sperry. In the Gone series, whenever he gets a Character Focus chapter, a lot of it is him admiring Lance and his looks. It's popular Fanon that he is gay but we'll never find out as he's dead as of Plague. Howard as well but following in the footsteps of Zil we'll never know since he's dead as of Fear.
Aziraphale of Good Omens, being an angel, after all, is an exceptionally gentle soul who enjoys the arts, never curses, has soft, manicured hands, and calls his demonic counterpart "dear." It's stated that one of the three first impressions people typically get from him is that he is very gay. In reality, he's more asexual.
Gilderoy Lockhart, a character rivaling Liberace in flamboyance, with periwinkle robes and his own line of hair care products. Of course it's most likely he's not gay or straight, but a narcissexual.
Colin Creevey. A popular fan theory is that Colin had a crush on Harry, due to the frequent comparisons between him and Ginny in the second book. In fact there's a rich history of boy-on-boy crushes at British boarding schools in both literature and real life, and this book goes into great detail on the matter as pertains to the lead-up to the First World War.
Theodora from The Haunting of Hill House lives with a female "friend," and seems to be very attracted to Eleanor. It's implied that Eleanor returns her feelings, though it may be because she's starved for affection.
The Hellfire Club by Peter Straub has the villain Serial Killer, Dick Dart, who exhibits a bunch of Camp Gay tendencies. He speaks rather effeminately, has the best fashion sense of all the characters in the book, and is big on makeup. In fact, one moment slightly hinted that he was jealous of women, and quite possibly even wanted to be one. The only thing is... he's only shown to rape women, and claims that he "adores" them.
Will Solace from The Heroes of Olympus. His bickering with Nico di Angelo comes across as Belligerent Sexual Tension in the last book, though it's left ambiguous as to whether it went anywhere. Nico, however, is decidedly less ambiguous and it's very clear that he develops a crush on Will by the end of the book. The ambiguity ends in the follow-up The Trials of Apollo series, wherein Will and Nico are an official couple, which Will's father Apollo approves of (and is a bit jealous of).
Eragon from Inheritance Cycle comes off as this, though his obsession with an unattainable elf girl indicates that he's straight. Despite this, he travels and becomes EXTREMELY close to his half-brother Murtagh, and starts getting vengeful and sulky when Murtagh turns out to think he's an annoying little twerp. Additionally he never notices Arya's sexual characteristics (read: breasts)note perhaps because he's the badass MAGIC CHOSEN ONE and thus above such things as staring at boobs, but he spends a lot of time ogling his master's muscles, "port-red lips" and long, flowing hair, and starts staring intently at the guy's "hairless groin" during a naked bath scene. He also ogles the "hard and lean" muscles of his crippled ex-nemesis, and even drops his pants (but not underwear) in front of his cousin to show a very intimately-placed bruise. Oh yeah, and he spends a lot of time fondling, rubbing and stroking wooden staffs, swords, and other fun phallic weapons.
Gutman, Wilmer and Cairo are all supposed to be varying shades of homosexual. Also Hammett's use of the word "gunsel" later in the book. From chapter four:
The girl returned with an engraved card — Mr. Joel Cairo. "This guy is queer", she said. "In with him, then, darling", said Spade.
Effie Perine: Her face is repeatedly described as "boyish" and she seems to have a crush on O'Shaughnessy.
A file on Francisco Scaramanga in The Man with the Golden Gun mentions he might be gay, judging by the fact that he uses a big gun, and that he can't whistle. However, it is mentioned that the latter example is just a myth.
The Merlin Trilogy: Ulfin is described as "self-contained in the manner of men who know they must live their lives out alone, or as the companions of other men", which is in some way related to his childhood slavery and sexual abuse. It's not clear if this means homosexuality or asexuality.
Ilke from Phenomena is either this or Ambiguously Bi, her Ship Tease with Jolsah is mostly from his side. Yet does it seem that she Likes Older Women by her weird over-attraction to mothers, and a slightly Romantic Two-Girl Friendship with Millian that sorta resembles Korra and Asami's the way it was in the beginning, expect in that Millian is in love with Azur, and they (Millian and Azur) become a couple, if it'll last is yet to be seen. Hisj has shown some interest in a Wife Husbandry way only to be told by her that she doesn't belong to anyone. According to Word of God is she not asexual either, but her type is someone as powerful as herself, and her being one of the most powerful characters in the series will it not be an easy task. And with Norwegian sharing words for both girlfriend and boyfriend, kjæreste (word he used for partner), meaning 'dearest', does it stand as ambiguous.
All three members of the main trio in The Picture of Dorian Gray have shades of this or Ambiguously Bi, but it is most significant in Basil Hallward. Whereas Harry is married and Dorian has female lovers, Basil never pursues a relationship with a woman, and it is indicated rather strongly that he is in love with Dorian. He considers his friend to be the model of physical perfection, takes him as the muse for all his art, and compares him to a number of mythological and historical figures known for their involvement in same-sex relationships. (As mentioned in the Les MisÚrables example above, this was a popular method of implying homosexuality in the days when outright discussion on the subject was frowned upon or forbidden.) Though tame by today's standards, the book was widely criticized as immoral when it was published.
Raffles has clothes horse/cricket player/master thief A.J. Raffles. He's handsome, lives with his roommate and partner in crime (Bunny), with who he has been very affectionate and flirtatious with, and to top it off, was made with the model of an outed gay of the time. Sure, he had a female love interest and had gone on a Roaring Rampage of Revenge when she died, but his confession afterward comes with the connotations of he'd be willing to do the same for Bunny.
A discussed trope in REAMDE. Zola notes that two of the terrorists who are holding her hostage are either a gay couple or have the closest platonic friendship she's ever seen. She wonders if they have sex when they go to bed together, but never finds out, and the question is left unresolved.
Redwall has this cropping up multiple times with Loads and Loads of Characters. Some of the most obvious examples include Clogg's reaction to Ballaw, who appears to be intentionally flirting with him ("D'you hear wot he called me? Sweet Cloggo. Ain't that 'andsome!"), Craklyn and Piknim's Romantic Two-Girl Friendship vibe, Sunflash writing poetry to Skarlath, and Ruddle and Folrig living alone in a cave together and taking every opportunity to wrestle/hug both each other and Sunflash.
Tom Ripley in Ripliad. In The Talented Mr. Ripley, he claims not to know whether he likes men or women, and jokingly says that he's going to give up both. In the same book, his obsession with another young man seems borderline sexual, although he ultimately becomes disillusioned with him and kills him to get his money. In later books, Tom is married to a woman, but his sexual attraction to her seems minimal at best. They sleep in separate beds and rarely make love, and he seems to treat her more as a trophy wife than an object of love. In The Boy Who Followed Ripley, he's clearly attracted to the 16-year-old "boy" of the title, but nothing ever comes of it. He rescues the "boy" from kidnappers while dressed in drag, but he seems more amused by this than sexually thrilled. Tom ultimately has little interest in sex of any kind, although he's clearly attracted to other men occasionally.
Gene Forrester certainly applies. He describes Finny's body, talking about how he moved like a panther. He also talked about Brinker's butt for an entire page. And Finny definitely loves Gene, and he has a few effeminate qualities.
Lets not leave Finny out of this. In one scene he watches Gene undress and when Gene is wearing nothing but his undershirt he says:
Finny: You should have worn that all day, just that. That has real taste
A Series of Unfortunate Events has Sir and Charles, in a very downplayed example. In The Miserable Mill, we are led to believe that they are simply business partners with an extremely lopsided distribution of power, with Charles being too meek to put his foot down to the more domineering Sir's cruel actions. They show up again in The Penultimate Peril, and the conversation the Baudelaires overhear is a lot more tender, with Charles timidly telling Sir that he cares about him, and trying to get Sir to reciprocate. When the hotel burns down, they're holding hands "so they don't lose each other in the blinding smoke". Then this (paraphrased) line from one of Lemony Snicket's love letters in The Beatrice Letters seals the deal: "I will love [Beatrice] until C realizes that S is unworthy of his love."
The Sissy Duckling is often seen as a gay allegory due to the protagonist. Elmer is a flamboyant, effeminate duckling who gets called a "sissy" by others.
Michael from The Traitor Game. He forms an extremely close friendship with Francis (who, for his part, is Straight Gay) and seems to notice all sorts of details about his hair, hands, eyes, etc. He never shows any interest in girls, though that could be because the story takes place in a boys' school. Word of Godsays that Michael and Francis would probably end up together, but it's unknown whether he is gay, bisexual, or thinks If It's You, It's Okay.
Aro, a more subtle example, who is very cheerful and constantly talks in a feminine manner. He certainly seems to like both his 'dear friend' Carlisle and Carlisle's adoptive son Edward...
And then he was played by Micheal Shean in the movies and all those subtle points get turned Up to Eleven
Noah Antwiller: Its like [the Volturis] spend all of their afterlife being as fruitily gay as possible.
Carlisle is more than a little of this. He's an extremely well-dressed (look at that coordinated shirt and tie in the hospital scene! That extremely sexy shade of blue!) has an immaculately clean and artistically decorated house, loves to cook (if only because, as a vampire, he doesn't get to very often) and has a lot of "foster kids" but none of his own. He's also a ridiculously pale, ridiculously blond bishonen. The wife proves nothing. He's also just a few years older than his "children" are supposed to be. You cannot tell me that if you saw him and Edward in a public place together your first thought would be that they were father and son. In fact, when Eddie's mom told him to save him, Carlisle changed Edward with the intentions of the two of them being companions. The flashback in the movie where he turns Edward is ridiculously full of subtext. In the books Edward mentions Carlisle spent a lot of time in Italy a few centuries back, were he hung out with a load of male vampires who were models for works of art. He left after he got sick of them trying to "convert him to their lifestyle" it wasn't just blood Edward meant.
There's also Kafrina and Senna of the Amazon coven, who are "like two limbs of one organism."
The two Romanian vampires in the fourth book were obviously meant to be a couple. It was a legitimate surprise when they...you know...
Depending on who you ask Alice could be perceived this way.
Maz, from the series Violent Blue, could be applied to this. It's revealed in the end of the series that he is a man, by his female fiance (who gets a sex change before they get married.)
Ravenpaw and Barley from Warrior Cats. They spend basically all of their time together, and one of the authors has stated (paraphrased) that "they don't want any she-cats bossing them around." But the biggest ones in this series are Tallstar and Jake. Ravenpaw and Barley could just be seen as Ho Yay if you didn't have the subtle implication from Word of God that they aren't interested in she-cats, but Jake and Tallstar seem to be in love without ever coming out and saying it. In this case, the authors do just about everything they can (short of actually outing the characters) to say that the two were together.
Both the main protagonist and Reese in What I Was by Meg Rosoff. Reese is borderline obsessed with the narrator, who, in turn, is borderline obsessed with Finn and speaks of him very romantically throughout the story. At one point, Reese is described as "choosing to agree with the unambiguously heterosexual majority" out of fear, which could mean that he's in a Transparent Closet of sorts.
While there's a plethora of Bi the Way characters and a MASSIVE amount of Homoerotic Subtext, Wicked has Tibbet and Crope. While neither of them are major characters, they are nigh-inseperable, very very VERY close and just sort of come off as... well, gay. It doesn't help that Tibbet had sex with a male Tiger in the Philosopher's Club (don't ask, you don't want to know) and Crope ended up in the theater establishment.
Young Wizards has Tom and Carl. They are senior wizards who happen to live together and own a few dogs and koi fish, but other than that, there wasn't anything else that put their sexuality into question. The author of the series later allegedly performed a Flip-Flop of God on Tom and Carl's sexuality with her allegedly stating to a private audience that Tom and Carl were gay but later took all that back, saying that Tom and Carl were actually inspirations of two close friends of hers, who were both actually straight