Naoi, after Otonashi snaps him out of his angst and gives him some sense of self-worth, makes frequent comments that can easily be construed as being in love with Otonashi.
Kazuki from Get Backers. He was raised to be like a woman, he looks like a woman, he has long flowing hair, he is always surrounded by men, and Ban jokes about him and Juubei being like a married couple. He did show interest in one girl, but she looks like a boy and is actually a computerized being. He has never said a word about marrying and having children, even though he's the heir to the Fuuchouin clan and all its associated combat arts.
Everyone in Gankutsuou, except Eugenie Danglars who is unambiguously straight. Extremely ironic, considering that she is as unambiguously lesbian in the original novel as 19th century literature could hint.
Tucker, though despite the way he dresses, he has a very deep, masculine voice, but still manages to be flamboyant.
Burgh, a fashion designer who wears tight pants and a scarf.
Zoey is usually claimed to be this, for her short hair and habit of dressing almost exclusively in boyish pantsuits for contests, and being very touchy-feely with Dawn.
James is often the subject of discussion as to whether he's Camp Gay (often crossdresses, campy mannerisms and obsession with his looks) or Camp Straight (crossdressers are usually hetero, straight Bishōnen often have campy mannerisms, and he's had several crushes on girls including [very briefly] the psychopathic Jessie-lookalike Jessebelle). The dub dialogue usually exaggerates the former while also adding a few confusing signposts in the other direction; given this is Pokémon, it's unlikely the question will ever get an answer.
Bugsy in Pokémon Golden Boys. He's a young pseudo-Bishōnen, even more so than in the games. He's constantly blushing and acting sweet around Gold. You may think this is just his personality, but he acts differently around other people.
Pokemon themselves are no exception to this. Meowth from the anime has a Foe Yay driven relationship with Pikachu (it changed to straight Ho Yay once), has had homoerotic fantasy spots about Giovanni, and has fallen for James on one occasion (due to mood-altering Shuckle juice). Ash's Oshawott has the same sort of adoration towards Ash as Chikorita, Aipom, and Gliscor had; the former two of them are confirmed to be female and in love with Ash at one point.
Daley Wong and Linna Yamazaki from Bubblegum Crisis Tokyo 2040 share both similar backgrounds and extremely ambiguous sexuality, though nothing is ever admitted outright. Linna's reaction to the resident biker chick and bad girl getting a boyfriend is telling enough however, as is the fact that she spends the next couple of episodes moping about it. Poor Linna...
In the original Bubblegum Crisis, Daley is openly gay, and would occasionally hit on his partner Leon McNichol in order to tease him.
Daley: You're too tense, Leon. We could get a hotel room together. Leon:(dismissive) Yeah, sure, Daley, just you and me.
Itsuki Koizumi from Haruhi Suzumiya seems to like invading the main male character's personal space a little too much in the anime, and in the novels especially he makes it quite clear that he trusts and likes Kyon. He claims to act the way he does because Haruhi expects it and would make it real if he didn't, which would be a plausible explanation if he actually did so while Haruhi is watching. Also, in the 4th novel his alternate universe self admits to having a crush on Haruhi, but this isn't brought up in the main storyline - although many of his actions and words towards Haruhi, especially his constant claiming of being "the expert of her heart" imply some secret affection for her. Whatever the case may be, Itsuki's bond with Kyon could be seen as a fumbled attempt at a bromance or an actual romance slowly developing.
Pegasus from Yu-Gi-Oh! (and not just the Abridged Series or the English dub). This one is especially weird because Pegasus is one of the most blatant examples on this page... and also quite clearly established as straight.
In Yu-Gi-Oh! GX, we got Johan/Jesse Anderson, Judai's new best friend who wears frilly shirts, uses the ace card Rainbow Dragon, and spends a little too much time with Judai for us to believe he's completely straight. His subtext with Judai is spread so thick that it's noted on in-universe.
Amongst the hollows, there is actor-wannabe, pink-haired, flamboyantSzayel Aporro Granz who becomes even more bishonen when he releases his sword, named Fornicarás (kanji: 'evil promiscuous queen/princess', Spanish: 'you will fornicate'), which he's also willing to deep-throat. His fights are accompanied by lewd, disturbing comments regarding the sexiness of his opponents and whether or not they're his type and when his clothes are damaged, he will stop fighting to get changed before continuing. He'll even use his cloning attack to give his opponents fashion make-overs.
General Blue in early parts of Dragon Ball. He is known to find women disgusting, Bulma and Krillin come right out and call him gay but he strenuously denies it, and barely an episode before he gets a bridge dropped on him, he's revealed to be Shotacon.
Dragon Ball Z has Zarbon, who has an extremely feminine face, keeps his hair in a long, loose braid, and wears lots of jewelry, not to mention shiny black thigh-high boots. He's also apparently rather obsessed with his appearance. Frieza is questionable as well, having extremely feminine mannerisms in the Japanese and an old-lady voice in the dub (though changed as of Dragon Ball Kai).
Goten and Trunks have been very tight friends literally their entire lives and, as teenagers, quite often spill over into Ho Yay. Trunks even shows no interest in women, and his mother went to the extreme of putting him in a office building shaped like a penis and filling it with hot women; he seems outright intimidated by both. Whether their being Fusion Dance partners makes this better or worse is debatable. In the second Dragon Ball GT ending, it begins with all the various couples being shown together: Goku and Chi-Chi, Gohan and Videl, Vegeta and Bulma, Krillin and Eighteen... and then cuts right to Trunks and Goten walking along, in the same style. Apparently the creators consider them "life partners" after one fashion or another.
At the end of Dragon Ball Z, when the Z fighters are competing in the tournament, Trunks is paired with a leather-bound muscle man who blows him a kiss and makes a comment to the effect of "Oh, I got the cute one."
Lloyd Asplund is certainly mechasexual and Prince Schneizel is more ambiguous. His Bishounen advisor Kanon lampshades both in R2 09. He likes talking about love for a war advisor, apparently.
Kanon himself, who is quite pretty and expresses more concern for Schneizel than an advisor should for a boss. Side materials state that he's a crossdresser who had a hard time getting a job until Schneizel hired him for his talents and didn't mind his peculiar tastes.
Rolo in the anime. While he states that he sees Lelouch as a brother, there's some scenes where it seems more like he's in love with him. This is to the point where many fans saw his murdering Lelouch's girlfriend Shirley and his intended murdering of Nunnally, Lelouch's sister, as a case of Murder the Hypotenuse.
Jakotsu, who hits on pretty much every male character he comes into contact with (except Bankotsu), and has an unwanted attraction to Inuyasha, to the point where, in his sadistic version of love, tries to torture him to death because of it. After The Reveal that Jakotsu was the only completely loyal member of the Band of Seven, Bankostu shared a bubblyHeadbutt of Love with him.
Jaken started following Sesshomaru because he thought Sesshoumaru was beautiful. This is anime filler only and never happened in the manga.
Ayame Sohma from Fruits Basket. Long, feminine hair; feminine clothing; has been seen wearing an actual dress. He acts rather romantic and melodramatic, and his voice (at least in the dub) is... well... stereotypically gay. He and Shigure hit on each other with alarming regularity. And yet, after all this, he's a totally straight pervert who is revealed to be dating his (female) shop assistant, Mine. Even Ayame's American voice actor basically said in the most polite way he could that he didn't want to portray Ayame as a Camp Gay stereotype because he didn't want to be offensive. There's also that one scene where Kyou wakes up to find Ayame sleeping next to him in bed. He goes into a shocked state and Ayame mumbles "I'm still sleepy", grabs Kyou and tries to cuddle with him. We then see him covered in bandages from after Kyou beat the crap out of him and Ayame states he snuck into Kyou's room because Yuki had locked him out of his room when Ayame tried to sneak in.
Ryu and Ken from Street Fighter II V. Swimming in a pool naked together, pulling each other's underwear and Ryu riding the back of Ken's motorcycle in a girly manner are just some of the examples of this. (This doesn't apply to the games, where Ken is married to Eliza and has a son, and Ryu is completely stoic about everything.)
Poland could be the poster child for this trope. The only thing stopping him from being fabulously Camp Gay is the fact that his sexuality is never stated or touched upon.
Italy has a high, girly voice (said voice being by the same seiyuu as the below-mentioned Fai and sounding quite similar), a tendency to sleep naked with his male "friend" Germany, when growing up he wore a dress and was often mistaken for a girl, and when younger (Chibitalia) he had a romance going with the (male) Holy Roman Empire. He still likes pretty women.
England is very tsundere, looks like a twink and is the only one of the main eight characters to never show interest in women — when the cast is asked what kind of girl they would like, he's the only one who doesn't answer, albeit due to a "loss of time". England has also had Ship Tease with several male characters, mostly the implication that he has a crush on America. There's also when he infiltrates Italy and manages to blend right in....until he doesn't flirt with the girls. And to top it all off, Word of God is aware of the stereotype that British men are gay.
Germany, another tsundere, is in love with Italy, and the fandom often interprets Buon San Valentino as Germany's Coming-Out Story. However, it's possible Germany is sexually attracted to women as well. To make matters more confusing, he is extremely awkward when talking with women or talking about women, which could be interpreted either way.
Russia is often shown blushing, giggling, winking, giving off a pink flowery aura, and sending "pressure" in the form of little pink hearts. He is implied to have crushes on at least three male characters, especially Lithuania and China. He also greets men with a kiss on the lips, but this is only because of his cultural traditions. Lampshaded by America, who declares Russia is a "bad guy" for this greeting, implying Russia may be invoking the Depraved Homosexual or Depraved Bisexual (and Russia "offers" to "make his gums bleed" after he says this). Lastly, there's that he refuses to marry Belarus, the only person actually willing to "become one" with him, even though he acknowledges she's a very beautiful girl...but this could EASILY be because she's even more mentally unstable than him, and his own sister.
Creed from Black Cat is never explicitly stated outright to be gay. However, pretty much every single character in the series notices his romantic obsession with Train (other than Train himself). He dresses in very flamboyant, feathery clothing, and is constantly seen with roses (he has a freakin' bath filled with them!). He also seems rather resentful and angry at most of the females in the series.
In Air Gear guys who ride on the flame road have a tendency for this. Kazu and Spit Fire are ambigous,Aeon however is not.
Touko from Kara no Kyoukai blatantly flirts with Shiki, calling her 'a cute young lady along her line of fancy' the first time they meet.
Escargon from the Kirbyanime.It's pretty clear by episode 55 that he's in love with Dedede; he even uses "aishiteru" in his song at the beginning of the episode, and it's known that "aishiteru" is a stronger way of telling someone you love them. He even gets all flustered when he finds out Dedede heard the entire song. In the English dub, he was voiced with an impression of famous Transparent Closet actor Paul Lynde.
Yuda/Juda from Hokuto No Ken, who wears makeup and frequently parades around in his underpants and talks about how beautiful he is. He's straight, though, and has a harem full of women, even if he does make some questionable comments about how beautiful Rei is.
Major Alex Louis Armstrong from Fullmetal Alchemist. He's never seen with any women, but this isn't a romance-heavy series, so that's not a strong indication. That said, a lot of his character traits—strong emotions and a preoccupation with bodybuilding and male beauty—fit a lot of Japanese stereotypes about gay men.
Garfiel from the Brotherhood anime, the only reason why he isn't officially acknowledged as homo/bisexual is because the series doesn't state that directly.
D.Gray-Man has Kanda, who has an easy-to-provoke personality, a Bishōnen design, takes a lot of care of his long hair, and has an apparent lack of interest in any romance. Ironically, in later chapters it seems almost certain that he isn't gay after all, and in a Fourth Wall Mail Slot interview Allen speculates that Kanda has no romantic interest in anything except Mugen, his sword.
Going into huge (Visual Novel only) spoiler territory with Umineko, but what's up with Jessica and Kanon? Did she seriously not notice she was in love with her best friend, who is usually female? For that matter, since Yasu's gender is so ambiguous, it's hard to tell which relationships in the series are straight and which are gay.
Kaworu Nagisa from Neon Genesis Evangelion. Kaworu's behavior towards Shinji (who is himself Ambiguously Bi) and their interactions have been hotly debated since the show aired. A homosexual subtext clearly exists, and is carried through to both Alternate Continuity works and some official artwork, but it's never made clear whether this is all there is or if more layers exist. Shinji, being so starved for affection, might see Kaworu as a parental figure or some other source of familial intimacy. On the other side, there's the possibility that familial and sexual affection may not be mutually exclusive for Shinji due to his desperation and traumatic upbringing. There are also arguments that Kaworu is just a Fish out of Water and does not realize that he's making suggestive comments, or that human sexuality is completely irrelevant to him since he's an Angel.
In Rebuild of Evangelion 1.0, Kaworu awakens on the moon to promptly say "I'm looking forward to knowing you, Shinji Ikari." As lampshaded with many lulz by the fansubbing group, the Japanese word used can mean "to know in the biblical sense". And right after that he says he's gonna make Shinji "happy" this time...
Approximately half of Rebuild 3.0 is devoted to Kaworu and Shinji's budding relationship before Kaworu is horribly killed. Kaworu describing them playing the piano together like they're having sex isn't even the gayest thing he does.
The manga mostly averts this, however, at least from Shinji's side; as he's creeped out by Kaworu's tendency to invade his personal space and tries to stay away from him as much as he can. In vol. 10, Kaworu uses a kiss to stop Shinji from hyperventilating during a nightmare, and makes advances toward Shinji which he flatly refuses. He later leaves Kaworu's apartment with very little in the way of a good-bye, which upsets Kaworu, although after Kaworu's death, he admits to himself that despite the way he acted, he was attracted to Kaworu, even though he knew he shouldn't like a boy like that.
Cross-dressing ballerina kick-ologist Mr. 2 Bon Clay is about as ambiguous as they come. To the point where it's his catchphrase.
Also, Kalifa is ambiguously lesbian.
Kyoya from Ouran High School Host Club, and Tamaki to an extent. They give backrubs and call each other "mommy" and "daddy". Tamaki may be more along the lines of Ambiguously Bi given how he seems to genuinely enjoy female company, but Kyoya never displays any genuine interest in the club's customers beyond what he can get them to buy.
When Tamaki calls the rest of the host club (other than Haruhi) the homosexual supporting cast, Kyoya is annoyed. However, he's only annoyed by the 'supporting' line, he doesn't seem to care that he was called a homosexual.
The relationship between Mori-senpai and Honey-senpai seems rather suspicious.
The twins Karou and Hikaru are as ambiguous as they come. They play up the Twincest angle for all it's worth for the benefit of their fans and to draw customers, but they're often just as close even if they don't have an audience or are completely alone. There's also the probable crush on Haruhi to consider, but that doesn't arise often.
Schrodinger, from Hellsing. The flouncy, feminine Cat Boy evades this list no longer.
Hunter × Hunter has Neferpitou, a male cat-humanoid chimera ant with a very feminine appearance and mannerisms.
Madara Uchiha's obsession with Hashirama is well established, and that was before it was revealed that the Sharingan is activated by a loss of love, and Madara's was activated when he broke off his friendship with Hashirama...
Nyankoi: Junpei's friend Haruhiko, at least in his mannerisms. He's been known to buy eroge manga and was the one to start peeping on the girls during a Furo Scene. However, he was all-too-willing to wear the maid outfit during the school festival...
Nanase from Honey Hunt is more than a little of this with his feminine looks, long hair always in a ponytail, skill at housekeeping and cooking meals, and pretty much acting like a nagging wife to his friend Mizorogi. At the same time he is also studying to be a make-up artist and hair stylist at a technical school. This is confirmed to be true in Chapter 21 where he outright admits to Yura that he's gay and in love with Mizorogi.
Father Jelice Bryah of Hatenkou Yuugi. Lampshaded by Rahzel "I don't recall coming out of some queer's stomach." (She said that because he was trying to be her father, but given the idiot of a dad she has, he is definitely a huge improvement.)
Kurotobi of Amatsuki. He constantly hits on Toki, calls him cute and touches him a lot.
Peacemaker Kurogane: Most of the characters are pretty strongly implied to be gay or bisexual. Heisuke makes more than a few references to men and boys he finds attractive or may or may not have slept with. Saitou, while he may or may not actually be interested in men (who knows with him?), is willing enough to pretend to be for information. And general dynamics of Ho Yay between various cast members aside, there are always Hijikata and Okita, who always seem just one step shy of being an Official Couple (with Hijikata's voice actor going so far as to respond to a remark about his character having given up romantic pursuits for his mission with, essentially, "Uh...no"). The shinobi Susumu often cross-dresses (quite convincingly) to gather information, blushes when Tetsunosuke mentions that he and Testsu are friends, and when Tetsunosuke offers him comfort by trying to touch his hand following his sister's death Susumu tightly grabs Tetsunosuke's hand in his. Lastly there's Pretty Boy Suzu, based on his fanboying of Yoshida's sex appeal and his relationship with Tetsu before becoming a Depraved Homosexual in the sequel.
Alois Trancy in the second season of the anime. He alternates between being Ax-Crazy and sweet and cheerful, basically flirts with Sebastian via leaning into him and pronouncing that he "smells good", is very attached to his butler Claude, treats his one female maidservant like absolute crap (he stabs out her eye with his fingers just for looking at him and later mocks her for it), dresses and acts very effeminately and flamboyantly and has a girlish face. Well, he was ambiguous until episode 5 where he outright flirted with Ciel, licked his ear, and stated that he "wants" him. And in episode 11 when he tells Claude "I wanted your love."
Also, Finny of Ciel's household staff: girly looks, wears barrettes in his hair, Keet, a bit of a crybaby, and tends to go into fanboy mode over Sebastian.
And Claude. It becomes painstakingly obvious after he brainwashes Ciel, though maybe he just really wanted Ciel's soul...
Sebastian, believe it or not. Exhibit A. Stilettos. Exhibit B. The way he stands and walks, particularly prominent in the first couple of volumes. Exhibit C. Doesn't he say he finds Ash more attractive than Angela? Exhibit D. And, of course, fighting over Ciel with Claude, which leads to both Alois and Grell implying that he's in love with Ciel. Sebastian doesn't deny it, and, in fact, agrees while fighting Claude in episode... 10? That he's not fighting for Ciel's soul...
Koushaku Chouno, better known as Papillon, from Busou Renkin. He dresses in a flamboyant outfit including speedos and a distinctive butterfly mask, and he certainly has a lot of Foe Yay with Kazuki.
Desslok from Space Battleship Yamato is supposed to be straight, and has slept with at least two women (Starsha and Mela). And yet he has male bath attendants who rub him down vigorously and then clothe him (no, really) and he hits on his generals. And he had an entire canon song written about how he and Wildstar are "bound together" and "unable to live with it anymore". And Zordar, who ignores his girlfriend who is right there and can see everything to hug Desslok. When she got revenge on Desslok and Zordar found out, he said he would have killed her if he wasn't so busy, and did kill her in the original as soon as he got an opportunity. Not to mention Talan, Desslok's faaavorite general, who begs to be sent to prison with Desslok and bursts into tears on the spot when he's told he can't. In Farewell, Sergeant Knox shouts "I LOVE YOU!" to Wildstar (at least in Japanese). Wildstar and Venture do some bizarre wrestling when they're fighting over Nova. Wildstar and Ryusuke also have a fight while the narrator says how Ryusuke felt such new feelings within him. It's like the semi-canon Cast Full Of Gay.
Moonlight Ladys Io Azuma: Disappointed his cousin by growing up to be a "pretty boy" instead of a "hunk", really into J-Dramas, somewhat flighty, seems to polish his nails...unfortunately, nothing keeps him from being a pretty boy. Averted in the visual novel, where he is the Gay Option.
Sugata Shindō from Star Driver. He does love and care for Wako, but nowhere has it been shown that this is a romantic love. Also, his professed "curiosity" about Takuto as well as his gay subtext-dripping conversations with Head are signs that are too big to ignore...
Konata of Lucky Star. Holy crap, you could write a book about this. Her room is covered in posters and figurines of moe girls, she talks about Miyuki's breasts (in a joking manner?), she is obsessed with adult dating games (but girls like those too... right?). She seems to have massive picture archives of moe girls classified into different fetishes on her computer, seeming to include pornographic images as is hinted at in one episode. She definitely admires the female form. She and Kagami seem entangled in some sort of love-hatequasi-romantic relationship. Konata, after Kagami give up her seat to her at a concert, seemingly touched remarks, "What is this feeling?" Konata seems to have only ever had female friends despite having interests which should win her plenty of male attention.
On the other hand, Konata enjoys working at a Cosplay Cafe where she claims to enjoy the attention of the male customers whom she says are "kind of like" her boyfriends. She also seems to mention wanting a boyfriend (maybe? hard to sort out the exact words she used. might've been "lover". It was more of a daydream thing anyway where she imagined herself as several Da Capo characters before being swept off her feet by a bishounen [and therefore ambiguously male] version of herself). She also commented that she doesn't really like giant robot shows for the action but just thinks the bishi characters are hot. Whether she's talking about the bishounen or bishoujo character is not clear, though, as she seems to be watching Code Geass when she makes the comment.
Fate of Mahou Sensei Negima!. In chapter 336 where he says "He (Negi) already belongs to me. Give up." and the end of the chapter reads "The strongest love (?) rival appears."
While Setsuna's Bodyguard Crush on Konoka can be seen from space, Konoka herself is far less definite, and whether she just liked to tease Setsuna or genuinely returned her feelings continued to be a mystery. At the very least they get a lot of romantic/sexual moments together, and the epilogue heavily implies they married each other.
Miki from Life, and by extent Ayumu too. Their bond can be described as being stronger than a simple friendship but it's not exactly romance either. Apparently Ayumu liked a boy in middle school but she's shown no interest in boys in high school (though she has good reason not to with all the trouble she's been having). Ayumu falls for a boy by the end of the manga and Miki said she has a boy in her hometown though..
Lucia from Venus Versus Virus. Nothing is said about her bond with Sumire, and it doesn't go anywhere on-screen, but it's heavily implied she harbors feelings for her.
Gilbert Nightray/Raven of Pandora Hearts is sometimes suspected by fans as having feelings for Oz. He's also quite feminine in appearance, the manga artist likes to have him dress up in girls clothes, and he has shown absolutely no interest in females.
And Vincent, is sometimes implied to have feelings for his brother Gil based on his affectionate Yandere obsession with Gil. And then there's his Long-Haired Pretty Boy appearance and hatred of woman.
Leo often teased Elliot for being so feminine, what with his knowledge about the language of flowers and organic soaps and all. Then, there's how Elliot isn't all that interested in women and one guidebook comic in which he gushes over Cheshire Cat, who is a Cat Boy but just drops the happy when Cat Girl Ada shows up.
Saiyuki: Genjo Sanzo is hinted to be gay as it shown in the first season that he did he not get mad at all when a gay drunk came on to him in a bar:
Guy:(Leers and holds Sanzo's face) You're so pretty that you look like a woman. GS:(Calmly nonplussed) I'm a man though. Guy:(Leers even more) I don't mind. GS:(Remains placid) Fool.
It should be noted that Genjo Sanzo is the grouchy antisocial type who is usually averse, rather violently so, to both physical contact and smalltalk even with his close friends, much less random strangers.
Kamui Den: Nowhere more ambiguously that with Ryunoshin and his young charge Miyagi Onya. Initially, the latter approaches Ryunoshin requesting that he become his "nenja" (a kind of mentor figure, but like the erastes of ancient Greece, with strong gay overtones). Ryunoshin says he has no interest in "shudo" (male pederasty), but recognizing the young man's purity of heart, accepts his request to form a special bond (chigiri) together. Of course, Shirato had to go and muddy the waters further by saying in a recap, that the two characters shared a bond of "shudo," which all but explictly labels them as gay lovers. Certain characters within the manga also seem to think their relationship swings this way. As they are never shown engaing in anything beyond mildly affectionate behaviour, it would seem they are in a platonic gay relationship...maybe.
L. OK, so he does watch footage of Misa Amane strapped up against a board for a long time and does confess "I could actually fall for you" to her, but that doesn't stop him handcuffing himself to Light, as said before, and Light is the only character aside from Watari to whom he gives his 'phone number.
Near takes all the Foe Yay Light had with L to a creepy, rape-y, one sided extreme. He calls Light a lot and then hangs up without talking, pulls... odd faces when thinking of Light and in the manga it's revealed that Near didn't entirely want to kill Light, he wanted to keep him. And that's before we even get onto the Foe Yay chemistry that is more commonly interpreted between him and Mello.
Mello takes this trope so far as to be mistaken for a girl by a lot of readers/viewers until he is referred to as a "he" by other characters. He does not, like the other senior Mafia men, cuddle up with girls, dresses in tight leather long before he rides a motorbike for the first time in the series, has a VERY girly fur-lined coat, ignores Hal Lidner's coquetry when she talks to him from her shower, speaks with a peculiar kind of tension when talking to Near and lives with loose-cannon geek Matt in a house full of mannequins. Did we miss anything?
The elegant, well-manicured, immaculately-dressed and long-haired Yotsuba employee Reiji Namikawa. While almost all the other businessmen are either cuddling up with Misa's modelling friends or having a drink in her flat, he's busy looking at the artwork. Oh, and he wears a silver heart-shaped ring.
Rem's strange (and for a Shinigami, highly unusual and controversial) relationship with Misa Amane. (She says it's platonic, but who knows?) She also dies for her to rescue her and keeps Light alive just to keep her happy. That's some serious platonism!
Sayu, Light's little sister, is Ambiguously Lesbian- she first says that she "doesn't want a boyfriend." Then she exclaims that Misa is "my type!" And she smiles when leafing through one of Light's magazines. The ambiguity here is that she does fangirl over Hideki Ryuga (the pop star), so she might be Bi the Way if the fangirling is sexual in nature.
Otohiko from Kamisama Kiss. He's an all around pretty boy that flirts with both men and women. He dresses in a stereotypically gay fashion (he even has a biohazard suit decked out in flowers) and his familiars are show-dogs with a heart shaped collars. Nanami even calls him a homosexual when they first meet but his actually sexual orientation has yet to have been revealed.
Sunny from Toriko is extremely flamboyant, obsessed with beauty, wears pink, and licks other men with his hair. He is also trying to steal Komatsu away from Toriko (because he's beautiful when he cooks).
Bio Booster Armor Guyver has it's fair share of moments.
Tetsurō Segawa has subtle hints of being possibly gay towards his Bromance, Sho Fukamachi. His sister Mitzuki has taken various opportunities to paint them in such light when catching them in moments odd moments such as holding hands with Sho when the two were reaffirming their resolve and friendship. To top it off, he is never seen hitting on women, never flinching or startled when a naked Sho pops up unexpected. Such as when in the manga a Sho clone pops up and he comments on why he's naked due to the heat, and later when being busted out of a prison cell in the anime. During the final episode of anime, he encourages and pushes his sister to greet a long thought dead Sho, only for Natski to ask her why he wont himself, which causes him to blush in embarrassment.
The evil Chronos organization is nearly an exclusively male operated with male exclusive male membership in high ranks and troops. This has led to some ambiguity amongst their leaders and ranks. Supreme leader Archanfel has a girly elfish appearance, and later ends up having a shared mind with and mutual loyalty to fellow Zoalord Imurikum. Imurikum in turn is often shown carrying a Archanfel in his arms. The "Hyper Zoanoid Team Five" members have a big deal of loyalty to one another, but Elagen and Zx-Tole are portrayed in the OVA to a high degree of this trope with lines such as "You have to hold on, I need your strength, I need you!" and "Oh, I'll do anything for you Elegan!".
Here Is Greenwood: Kazuhiro Hasukawa, the older brother of main character Kazuya. Has a rather bishounen look to him and the rumors fly about his sexual orientation (he's the nurse in an all-male school). But then again, he's also Happily Married (and the wife is just another of the points of contention the brothers).
Kyouko has a lot of signs of having a crush on Sayaka, and her and Mami are shown to have been very close in Farewell Story and Different Story, but again there's nothing official.
Speaking of "knife edge between subtext and text", Lyrical Nanoha has the ever-popular Nanoha and Fate, who did all that Madoka and Homura did and more, outright adopting a child together. Again the staff love heaping on the Ship Tease, and there's semi-official Word of Gay from their voice actors, but explicit confirmation seems forever out of reach.
Moe Morita / Flamenco Sapphire from Samurai Flamenco. She frequently blushes around Mari, an older girl in her idol group, and reacts dreamily whenever Mari playfully kisses her. At one point she's shown expecting a kiss from Mari, and not only becomes visibly disappointed when it doesn't happen, but later states that she doesn't mind being manipulated by her.
Miku Kohinata from Senki Zesshou Symphogear is this. At first, anyway. Any ambiguity disappeared in G when episode 10 revealed that the reason she could link up with Shenshou Jing is because of her love for Hibiki.
Kaorin in Azumanga Daioh, though the "Ambiguously" steadily breaks down over the course of the series and becomes Transparent Closet (though she claims it's a case of Single-Target Sexuality). It starts getting lampshaded by the other characters including one point where Osaka just flat out asks her if she's gay or not.