Big-time between Vinnie and Rabbit from Skins. They argue Like an Old Married Couple and Rabbit often bites Vinnie when sparring. Considering Rabbit is a Smoke who find blood an aphrodisiac, that in itself is suggestive. In a flashback scene, after a teenage Vinnie wins a fight by ripping out his opponent's throat, he shoots a hot glance over his shoulder at Rabbit to see if he’s watching. They were also prison cellmates and everyone know how that works-
Noblesse is filled to the brim with androgynous men who like to remind each other that they are hot. Potential (one-sided) ships include, but are not limited to, Frankenstein/Rai (most obvious & consistent), Regis/Rai, & M-24/M-21, Previous Lord/Rai.
Jolly Jack himself draws suggestive but non-canon pics of Kat and Scarlet, and one of Kat and Van.
Monsterful has Topaz Gem and Samantha Thing, two 19 years old sexy Monsters, With Topaz taking a "dominant" role in their relationship as seen on this page for example. However it's stated that they're just very close friends, and Topaz just loves to play with Samantha in that way.
Heartcore. Volaster/Royce, which is not only canon but also how Volaster's successor Carval came into being. Then there's Ame/Ryo, which the author lovesteasing.
For someone who was apparently straight, Robin from Shortpacked! sure left her fingerprints on a lot of Les Yay moments and tried to set up a lot of male Ho Yay ones. A classic example. Then she came out as "straight with an exception", even though her inner monologue shows she had at least one other girlcrush ( Amber) besides Leslie.
Chapter 34, in the midst of sinkingAnnie/Jack, has a very awkward moment between Kat and Paz, and sneaks in an Annie/Kat Ship Tease at the end. Most tellingly is Tom's strange response to Kat's "me neither" line (in response to Paz thinking she's a lesbian).
Eight chapters later, turns out that Paz has a crush on Kat, and confesses this to her. They start going out.
Kat's attraction to Birds has been a Running Gag since Chapter 13. However when considering that "Bird" is a common British slang word for ladies, one wonders whether or not this was a sneaky case of foreshadowing.
Zimmy and Gamma: A muchstrongercase can be made for these two, the author's commentary refers to Gamma as "The only thing Zimmy could ever give a damn about", and even other characters acknowledge it. However, Tom has also said that they're not a couple "in the way you're thinking" on his Formspring, which he later clarified meant that they were together romantically, but not sexually.
Ysengrin and Coyote: Tom confirms that Y loves Coyote very much. It's unclear if Coyote reciprocates.
The two forest fairy girls are also very touchy-feely with each other, although it's more of a dysfunctional friendship. And it could be just because they're fairies.
Shadow 2 and Robot. Shadow has shown visible sadness whenever Robot mentions his "angel", Kat, and is clearly very uncomfortable with his protectiveness of her. (Although that might have something to do with the fact that is was bordering on stalking for a while there.) In chapter 35, after the two of them are severely injured, Robot fully realizes his feelings for his friend.
Robot: Oh, Shadow... Why didn't I realize it before? I love my good friend Shadow.
Also, Sonya and Yuki both lust madly after Zii. And Yuki once thinks that Didi is in love with her and acts flattered and says she thinks Didi is "hot". She also hugs Didi while blushing and putting her face into her breasts while naked.
Sandra and DiDi once enter a relationship and DiDi kisses Sandra and they go as far as to try to have lesbian sex with each other only to conclude that they're "two naked straight girls with poor boundary issues."
Zii also masturbates in one scene watching all-male pornography while calling Di Di's name.
Aparently Zii is well known to several female strippers in the city.
Also Camp Gay and Wholesome Crossdresser Dillion is trying his best to get in Gary's pants. It's so blatant that both Dillon and Zii seem to have trouble understanding that Gary is completely straight and has no interest in men. Dillon even seems to think he and Gary are in a relationship.
Menage a 3 frequently serves lesbian and gay hijinks with abandon.
The author himself supports Tedd/Elliot shipping, and has drawn them kissing at least once. And some of the filler, and has shown Tedd's female counterpart in the EGS:NP continuity, Tess, dating Elliot. Word of God states that in every alternate universe where they are able to do so, Elliot and Tedd are a couple.
And in at least one such universe, Grace hooked up with Sarah due to Tedd being off the market.
Also, Rhoda and Diane - hugs, normal, loking deeply into each other's eyes, OK, Diane calling Rhoda cute...hang on a second!
Torg and Riff from Sluggy Freelance. Also, this strip is a good (much rarer) Les Yay moment for Zoë and Gwynn. And though it almost certainly wasn't intentional, the fact that a guest artist had to put the words "NOT MY GIRLFRIEND" below her roommate says something... Lampshaded in this comic.
Josh Phillips' comic Avalon, had Pheobe Bradley, a girl whose sexuality was often left ambiguous and played around with. She had a lot of very close moments with her good friend Ceilidh, which eventually culminated into a Last Minute Hookup in the text-based epilogue posted after a long hiatus.
In the comic's old days, guest artists often came in to make little "joke comics" and other such things. One such guest artist drew up the Love Dodecahedron consisting of every teenaged main character in the series, and then made a little strip of the characters' reactions. Joe, the (arguably) lead male of the strips then said, "I think he forgot about the pink line between me and Alan." Pink lines in the dodecahedron symbolized "possible attraction to," with red lines as "definitely attracted to," and brown lines for "absolutely can't stand."
Screw that, Jigsaw and Addy kissed! Okay, Jigsaw was technically feeding on Addy, so it's more of a one-way relationship, but...
Sandra and Crystal from Zebra Girl. In Sam's universe, where he's the alternate of Sandra, he's in a relationship with Crystal's counterpart; he's quite confused when she gets a boyfriend.
Ping and Miho in Megatokyo, in spite of Mr. Gallagher's statement that only one female character, Sayuri, is attracted to other females. Come on, Ping went crazy when she thought that Miho was in danger. Twice. Despite her dark and manipulative personality, Miho's done surprisingly kind things for Ping, like take her out to eat multiple times, take her to a bath house, bought her underwear...
And it's hinted that Miho knows that Ping is anatomically correct. Hmm...
Miho toys with the emotions of others for sport. Just because she isn't attracted to Ping is no reason for her not to try and seduce her. And just creating the appearance of a relationship would be a great way to mess with Piro; see the "anatomically correct" comment.
She knew that Ping was anatomically correct because she went to public baths with her. Ping herself confirmed that she has all the human parts, later on.
For a supposedly straight girl, Miho has a lot of this. Her former best friend Junko acts like an embittered ex-lover towards her, and more recently, people have been seeing this between Miho and Yuki.
And back when she started her online relationship with Piro she briefly thought that he was actually a girl.
Given that it's unclear about Vaarsuvius' true gender, it's easy to see Ho Yay between both male and female OOTS characters, and fans most certainly have seen both, including between V and Belkar thanks to an Accidental Kiss, as well as with Haley. Since we don't know the gender of V's spouse either and their children are adopted, it's possible V actually is gay. The background during the Darth V transformation was a pink triangle ...
When Roy takes several arrows for Elan, and his "logical" excuses for doing so don't pan out, Elan exclaims "You like me! Roy likes Elan" and Belkar starts singing "Roy and Elan sitting in a tree..."
One of Haley's cryptogram confessions to Elan is "I've kissed a girl once.. no, more than once", and the anthropomorphic personifications of the various parts of her psyche includes Latent Bisexuality who apparently just sits in the corner most of the time.
When Miko is imprisoned after killing Lord Shojo, Sabine (also imprisoned) says some very interesting things to her.
An odd half-example: while Roy is transformed into a woman by a gender-bending magic belt, Belkar (who knows it's really Roy) takes delight in hitting on Female!Roy. He claims that he's only doing it to freak Roy out. . .
Gannji and Enor have a bit of this during the gladiator arc. The arc in question began with the slavemaster warning the new gladiators of "strong homosexual overtones that will not be fully explored" if a stronger gladiator defends a weaker one, and, according to Gannji, "I wouldn't last two days in this place without you to protect me." Then this ... It doesn't hurt the case that the "Lizardfolk Victory String" Gannji gives Enor is red.
Durkon and Malack are just friends, but in 871 Durkon finds out that Malack is a vampire, and then in 876 this happens.
Arguably, there's nothing in this moment that could be construed as anything other than Les Yay.
Lust and Pride/Fortune from The Sins... well, what do you expect from an Anthropomorphic Personification of Lust (who's only had sex with two people, one of whom we know, but still...).
Dora of Questionable Content (who is self-admittedly bisexual, while spending most of the strip in a monogamous relationship with a man, and making occasional reference to "ex-boyfriends" as a group and only mentioning brief flings with women) occasionally has these moments, particularly here, here and here.
See also here and here. (Read 'em both to the end.)
Then there's the Hannelore/Marigold (Hanigold?) subtext, which Jeph has addressed, and denied.
The time Mike kissed Dave, and the arc where they pretended to be dating...
The dialogue in the explanation segment towards the end of the storyline in Suicide for Hire where Hunter defends homosexuality by holding a fundamentalist protest group at gunpoint has some undertones of Have I Mentioned I Am Heterosexual Today? along with his given reasons. (Said reasons are that he's offended by seeing people misuse the faith he was raised in, and that he can't stand than the idea of the "Religious Wrong" - his words - being allowed to have their own way in running society at large.) Some may say the truth of his statements may be proved by the way he reacts to the waiter in the next section, but the waiter's behaviour comes under the heading of sexual harassment, which anyone would react badly to. Then there's this strip. And this one.
Furry webcomicLas Lindas has Alejandra Coldthorn and Tootsie Roswell. It's heavily implied, both through the comic and in the comic's forums (via Word of God), that Tootsie (Alej's longtime assistant and confidant) is gay for Alej, even if the feeling isn't mutual. She even has a way of calming Alej down when she gets angry — to keep hugging her until Alej says the safeword (which is "milkduds"; it's meant to refer to the snack, but Alej is a cow-like creature, so take it as you will).
And then there's this image of cast members Randal and Miles; on the forums for the comic, it's a running joke that Randal is gay, and this April Fools' strip was done to acknowledge the joke (and offer a little fanservice for those what wanted some male-oriented fanservice).
Also, Clarisse evidently considers Hazel/Thea inevitable despite Hazel's cranky insistence to the contrary.
Alex and Lita from The Wotch: Cheer!. Starts with Lita putting a ticket in Alex's tin for the "Win A Date With A Cheerleader" raffle, continues with her making an outfit for Alex to wear on said date, and only takes off from there. WithSleep Cute!
Soon after aforementioned Sleep Cute, Lita immediately deduces the dream she is in isn't hers when she notices Alex is "wearing way too many clothes".
Fighter and Black Mage in 8-Bit Theater. Fighter is endlessly devoted to Black Mage, following him across the planet and willing to oppose and/or attempt to kill anything that threatens him, behaviour which can't be entirely explained by his naivety (especially considering the rampant hints he's practicing Obfuscating Stupidity), while all of Black Mage's extremely rare Pet the Dog moments have either White Mage or Fighter as the focus, the former of whom he sexually propositions regularly. It should be noted that at the end of the comic, Black Mage and Fighter are the only Light Warriors who don't split up.
There was a hilarious bit where Black Belt faced a tentacle monster, was convinced he saw a penis, and then protested to White Mage throughout the next strip that he wasn't gay; he only thought he saw THAT, not that he's obsessed with phallic imagery or anything.
There is much evidence for Hope/Faith. Hope states that she and Faith were "perfect for each other". She likely meant it in an innocently friendly way, especially since they're young girls. She also seems to be the only person Faith's age who is accepting of her cat ears (birth defect, apparently) and likes to touch them (to Faith's bemusement). Though Faith doesn't mind Hope's company she isn't entirely comfortable around her due to not being used to having a friend.
When it was revealed Hope's parents abandoned her and Faith's sister Sara decided to invite her for a "sleepover" (planning to find a family-member to take in Hope), Faith was none-too-amused, but seemed to warm up to the idea. Later Hope was able to use none-too-subtle reverse-psychology to convince Faith into letting her sleep in Faith's bed instead of in a sleeping-bag on the floor. They are much too young to really have anything between them (and Hope did say they would have to "talk about boys" during their sleepover, though that could mean anything... right?). After Hope fell asleep, Faith's thoughts were as follows:
Faith (thinking): So here I am at my first sleepover. Man this is awkward! I barely know this girl and I'm sharing a bed with her. * sigh* I'll never get to sleep.
In a very, very, VERY Squicky manner, when Faith's aunt Desirae hugged Hope due to the young girl being absolutely adorable and very huggable, the following um... exchange occurred once the hug was over:
Hope: Your chest is really comfortable.
Desirae (looking rather sheepish... maybe even FLATTERED? Desirae! You're, like, old enought be Hope's mom! Literally!'): I get that a lot.
Hope once again showed a, err, interest in Desirae's chest in the one-hundredth-comic of the series, in which the characters broke the Fourth Wall (...and not for the first time) to celebrate. Unfortunately, they had no ideas; Desirae then spoke with "I could always show them my boobs!". After a bit of arguing over what to do, Faith interrupted and said they should all just reflect on what they have already accomplished. After a beat:
Marty (being a... fan of Desirae): I'm still for Desirae's boobs.
Hope: Me, too.
BLU Scout in Cuanta Vida seemed much more upset that BLU Spy wasn't gay than the whole "developing an escape plan with members of the RED team" business. Seems Spy might not be the only one spending a lot of time in closets.
Captain SNES: The Game Masta' Ryan and Alex.... Just Ryan and Alex, what with what he did twice in the presence of Ryan. Even the cat agrees.
Bass thinks that Vegeta and Green are going in this direction.
As perpetually bickering buddies from the opposite ends of the political scale, Sam and Alistair from Newshounds have had some moments.
Agatha and Zeetha from Girl Genius definitely have something going on. (For example: "We are kolee-dok-zumil. I know you.") Also, there's some definite Foe Yay between Gil and Tarvek.
In this page one of Agatha's beaus Tarvek states that he is about to 'senselessly pound' the other. The second beau sarcastically replies 'Ho, Yeah. Merry Christmas to Me.'
Then there's that Gil and Tarvek are Childhood friends turned rivals, due to a misunderstanding and Tarvek at least still keeps secrets that he felt would ruin Gil's life. And he'll kill Gilif Gil dies, so there's that.
For most of the latest story arc, they've been alternating attempting to throttle one another and brilliant teamwork that saves both their lives. Looks like they might be heading for a Wolfenbach-Storm King-Heterodyne triple alliance (hehheh) to forge a new Pax Transylvania. But be that as it will, Gil and Tarvek's relationship is going somewhere epic.
Kobayashi the Discount Ninja and Radd's Evil Twin Gnarl from Kid Radd happen to be standing on the same bridge, complaining about Radd, when they notiice eachother. They have a fantasy sequence of co-operating to bring down their common nemesis, but the fantasy starts moving into rather different waters, at which point:
Heightened quite a bit in the February mini comic, where Doc Worth sees Conrad at a cafe and visibly decides to tease him for a while, ending with him slicing his palm and giving Conrad (a vampire) a shot of blood for his espresso. Conrad drinks it.
Promptly made even more obvious where Doc Worth wakes up, incredibly grouchy and hungover in his office, and one of the first things he immediately asks Hanna is the whereabouts of 'Count Fagula'. Cue brand new nickname for Conrad, for one thing.
Hanna and everyone, essentially, but especially Hanna/Zombie. Both get really upset when the other one's in danger, they live together, and Zombie apparently makes him breakfast.
Also, this page with the good doctor and Chuck Goodrich. Hastings lampshades it in the alttext.
Living With Insanity has this moment and apparently there was supposed to be one here but it's probably nothing. Although, ever since Paul was turned into a bishie, he's been drawing himself naked a lot more often, so who knows?
Despite the obvious heterosexual partnerships flying back and forth during the plot of Bittersweet Candy Bowl, there's a tiny hint of this between Mike and Paulo. Played with during the summer arc, when they're forced to share a room. And a bed. Yeah.
The comic also has plenty of pretty blatant hints towards Quain'tana and Ash'waren's involvement with each other, as well as subtler hints between Ariel and Faen. And ofcourse there's the absolutely confirmed relationship between Mel and Shadnya.
Sister Claire depicted Claire and Gabrielle in a The Graduate tribute pose, Gabrielle persistently calls Claire "sweetie", and at one point, thanks to Gabrielle's unfamiliarity with mortal idiom:
"Now, let's have a girl-on-girl talk." "Girltalk?" "...Right."
Claire blushes nearly every time they meet, though that may just be a nun's reaction to, y'know, her boobs.
The Dreamer: Alan/Nathan. Especially when they fought. And don't tell me you can't see Knowlton/Alan or even Alan/Hamilton!
Despite the fact that they are just friends, there's the occasional scene between Shadowgirls' Lin-Lin and Becka thatjust, um...
This trope seems to be in effect whenever Yuudai and Taisei are alone: Taro leaves to spy on Jiro in disguise and Taisei and Yuudai find themselves alone, waiting for him. Then Taisei is exceptionally nice to Yuudai, making him compliments. Yuudai doesn't believe him at first, and when he finds out he is actually genuine with his kindness, he blushesheavily.
Slightly Damned: Rhea. Oh Rhea. She makes a joke trying to avert this in one comic where she's sharing the same bed with Kieri, and then is...passionately...kissed by Eve the fairy. On the male side, Darius had a crush on Kieri's uncle, and it was implied that Cliff and Duster may have kissed once.
Mayonaka Densha: There are many hints that Jack's feelings for Tom might go a little bit beyond friendship, especially given that Jack is a complete mysogynist. Which Hatsune will not shy away from mercilessly teasing him about.
"I'm sorry, I couldn't sleep over the sound of all this homoeroticism"
There's also the occasional Les Yay vibe between Irene and Hatsune.
Fishbones has some and it's even lampshaded by one of them.
In Something Positive, between Davan and Jason, Peejee and Aubrey, Peejee and Vanessa. For all three of these the author has made specific asides to point out that no, they're not going to happen. Also, Kestrel mistook Nancy's attempts to steal her panties on a trip to Provincetown for an attempt to win her over - her past experiences with Angela and, to a lesser degree, Kim probably didn't help. Then there was Mike - in the words of his therapist: "Well, Mike, while there's nothing wrong with accidentally catching your brother masturbating to gay porn, the fact that you've snuck back seven more times to see it makes you what we in the psychiatry field refer to as 'fucked up'." And Mr Sanderson greets Davan with a hug:
"I thought I'd never be able to do this again!"
"You know, the hug is uncomfortable enough without the orifice-tightening insinuation that it's taken place before without my knowledge."
Spinnerette, especially after Mecha Maid's recent confession. See the comic's TV Tropes page for more details.