Alan/Thomas. Alan writing Thomas into his manuscript as his savior figure. (Or vice versa.) Thomas, the Light Presence, saving Alan from the cabin and "keeping him safe through the night". Episode Four ends as Alan finds what he needs to defeat the Darkness, the "clicker" left by Thomas who knew Alan would need it, and the credit song is "War" by Poets of the Fall, a sort of romantic power ballad with lyrics like "When I thought that I fought this war alone, you were there by my side on the front line" and "we were one with our destines entwined". It might be referring to Alice, but she's trapped at the bottom of Cauldron Lake.
Barry and their Heterosexual Life Partner relationship. At the end of the first telephone conversation he hangs up "I love you" and after he joins the story physically (NB: he flew over to Alan the moment he felt something was amiss) he takes Alice's previous role (i.e. being a damsel/sidekick combo).
In Alpha Protocol, if protagonist Michael Thorton gains a good enough relationship with one of his handlers, Sean Darcy, Darcy will give him a signed photograph of himself as a gift. After the "Operation Desert Spear" phase of the game is completed, Mike will keep the photograph next to his bed in all of his safehouses.
Alexander and Daniel in Amnesia: The Dark Descent. Alexander speaks tenderly to him and is surprisingly attached to him despite the fact that Alexander isn't even human and sees humanity as insects. Mega points for Alexander waking him up for a nightmare and comforting Daniel in his bed.
Arcana Heart is filled to the brim with it. Being an all-girl fighting game, this is to be expected. By Arcana Heart 3 it can barely even be called subtext anymore, particularly where Heart and Saki are concerned. Clarice's crush on Elsa also goes well beyond subtext and everyone accepts that she's flat-out in love with her, and Mei Ling Hua and Mei Fang are a classic Pygmalion Plot.
Rios and Salem of Army Of Two, to the point Mission Control probably sees them like this given the way she doesn't buy into their machismo. Rios' "wife" figures into the graphic-novel prequel, where they are never actually shown getting married, because Rios would always run off with Salem on missions on the wedding day. When Rios and Salem ask for time off to vacation in Hawaii together, Rios' wife hasn't even been mentioned for quite a few pages.
In Assassin's Creed II, the main character Ezio is best friends with a young Leonardo Da Vinci. With the way Leonardo's eyes light up every time he sees Ezio, the insistence that Ezio road trip with him to Venice, his shooting down Ezio's dreams of hooking up with (then married) Caterina Sforza a little too insistently, Leonardo's relief that Ezio's still alive after constantly putting himself in danger, the passionate hugs they share (including the famous Quick Time Event) and after 22 years he's still arguably Ezio's closest friend, enough that the Assassins trust him implicitly with the secrets of the Order despite his not actually being a member, it isn't reaching at all to see at minimum a one-sided crush on Leonardo's part. (Keep in mind, historians are pretty certain that the Real Life Leonardo was gay.) Whether or not it's reciprocated on Ezio's part is debatable though, and good arguments can be made either way.
In both Brotherhood and Revelations, you can send female assassin recruits on missions of the "Steal a Kiss" type, which involve seducing a Templar supporter's wife.
In the DLC The Da Vinci Disappearance, Ezio has to go retrieve Leonardo's "Assisstant" who himself is fairly flamboyant, the two share a conversation littered with the assistant ending up thinking that Ezio is into him. There's also a conversation about the Mona Lisa:
Leonardo: I work on the small portrait of a woman. I am growing rather fond of it. Ezio: Do not let a beautiful girl distract you from constructing my designs. Leonardo: Have no worries. Women provide little distraction. Ezio: Wait, I don't get it.
Assassin's Creed III has Haytham Kenway and Charles Lee. Charles spends the first part of the game essentially worshipping Haytham. After Haytham's death, his behaviour is turned up to eleven, and his confrontation with Connor immediately afterward heavily suggests that Charles loved Haytham. During the segments in which Haytham and Connor work together, Haytham frequently talks about Charles' good qualities, and talks at length about how he feels Charles is much better than George Washington not only in terms of leadership and military prowess, but personality as well.
The Avernum game series has this BROADLY implied between two NPCs.
In BioShock Sander Cohen practically flirts with you as you try to complete his little art project, and nicknames you "little moth". Sure, it's creepy because it relates back to the disciples he had and is now killing off, but it seems rather personal. And then there's Atlas/Fontaine. He seems so nice, you start to trust him... and bam! Turns on you, but he keeps talking to you, comparing you to a dog has to be put down, and he seems honestly upset about the thought. Then "Danny Boy" is playing in his apartment. Sung by a male singer, too. It's like the developers want you to embrace the screwed-up relationship!
BioShock 2 has an audio-log from Stanley Poole, in which Stan describes how he needs to be "more like Johnny Topside" (Delta pre-Daddy suit). "I keep thinking of Johnny Topside, though. Took real guts to find Rapture like he did... makes it easier not to crack if I sort of... imagine that I'm him. It's a good thing I can't tell Lamb about that. She'd probably say I got a secret need to fall into his arms and make wild whoopee or somethin'!"
The Brute Splicer, who Word of God all but outright states is an Armored Closet Gay. He seems to admire Sander Cohen ("There was a man! Smart suit, took no guff!), and when using the Charm plasmid on him, some of his lines towards Delta get downright flirtatious.
Taokaka's favorite things in life seem to be, in no particular order: family, food, sleep and big breasts. She enjoys fondling and burying her head in Litchi's "airbags," tells Noel she should eat more meat buns to "make her boobies bigger," and spends much of Continuum Shift eating, sleeping and groping every other female character she comes across, even asking Bang if he's visiting Litchi's clinic to fondle her breasts like she is. "Oh Boobie Ladyyyy, where aaaare yooou? I wanna play with your bouncy boobies!"
She's not limited to groping Litchi's breasts, either. In Continuum Shift Tsubaki becomes a victim of Tao's ravenous lust for boobies. Noel would be as well, if she weren't flat-chested, something Taokaka has to make a point of mentioning every time she sees her. To round out this list, Chronophantasma sees Tao looking for "Lacking Lady" on Ragna's behalf only to end up groping Makoto in the latter's Arcade mode.
It's hard not to envision Litchi Faye Ling as Ambiguously Bi given her propensity to dress other girls up in cute outfits and dote over them (Noel in Calamity Trigger, Tsubaki in Continuum Shift, Bullet in Chronophantasma). She is the most common target of Taokaka's breast groping, and seems almost tolerant (albeit embarrassed) of it on a few occasions. In a non-canon segment, Litchi was apparently very... "thorough" when examining Noel's "beautiful, lithe" body in a Teach Me, Ms. Litchi: Reloaded segment... and doesn't realize she was being so "thorough" because it was like "a dream come true".
Noel has become quite a case of Even the Girls Want Her, as Litchi has a fetish for dressing Noel up in cute outfits, and Makoto is extremely protective of her. There's also a lot of official(!) Noel X Rachel art.
Noel and Tsubaki, especially on Noel's side. Even with Tsubaki trying to kill her, Noel cares for her friend so much, that she has to love her, platonically, or romantically. She even became Mu-12 again, just to save Tsubaki, despite the traumatic memories associated with this transformation.
Jin is... a leetleobsessed with Ragna. "Ah~! Long time no see...BROTHER!!!~"
Jin's obsession is played with a lot in the various gag reel endings in the story modes - even in those for mostly unrelated characters. In Teach Me Ms. Litchi he has hearts over his head and in his eyes every time Ragna speaks. From Relius Clover's CS Extend gag reel, where he mind-swaps several of the other characters, in particular Ragna and Jin:
Jin: Is... is this... Brother 's body...?! *Pant* *Pant* Oh, Brother... BROTHER! Ragna: NOOOOO! Hand-check, Jin! Hand-check this instant, you freaky—! Jin: Finally, I'm where I've always wanted to be... inside Brother's body...! *Sniff* *Sniff* It 's like a dream come true...! Ragna: This isn't real...! Nope! I'm dreaming, and I'm gonna wake up, yeah?! Somebody pinch me—dammit, Jin, not YOU!
In Jin's joke ending of CS, he's trapped on an island with 3 fake Ragna clones. The first thing he does is tell Noel to leave, and that he's going to have fun. In Chronophantasma, he ends up back on the island, and insists that his feelings for Ragna are entirely murderous in nature, but the Ragna clone doesn't buy it. The clone admits to being slightly curious towards Jin as well (then again he was created from Jin's imagination).
In episode 2 of Teach Me Ms. Litchi Again of CP, Jin constantly pesters Ragna for a "body examination". He also agrees to teach Tao in exchange for a method in catching Ragna. The last we see of the two is Jin dragging tied up Ragna off to do god knows what with him.
In addition to the Manly Gay accusations Azrael faced on BlueRadio, during Bang's Chronophantsam gag reel, Azrael confronts Jin on the size of his inner man during the first round, where Jin is nearly dying from the heat.
Luna: What the? Are those two gay? Are they?
In Bully, main character Jimmy really can kiss some of the other boys in the game. Then there's that time Petey Kowalski makes an excruciatingly painful joke about Jimmy becoming a male stripper.
In Castlevania: Order of Ecclesia, when the (very female) Shanoa rescues Monica, the seamstress, she responds to this with "What did I do to deserve being rescued by such a beautiful angel?" If this sounds like a romantic come-on to you, you're not the only one. Most of her other interactions with Shanoa have more muted levels of this, and she has some interesting bits of self-loathing going on. It's not exactly hard to read her as a closeted lesbian.
Even the Liliths in the castle get in on the Yay ("Let's play, cutie!"). The Werebats, too ("Let's play, cute little kitty~"), AND the spider-women. ("You look DELICIOUS!" They ARE trying to eat you, but they still say it in a very lustful way.)
Likewise with the jeweler Laura: "I never managed to touch your heart, though I learned a few things about my own..." Everyone's les for Shanoa!
Laura: You dress like you're in mourning. Waste of such a finely-shaped— Shanoa: Enough of that, thank you.
The always-together antagonists. Death is Dracula's confidant indeed... "Dracula's intimate friend"? "Knows many dark secrets"? Okaaaay... Thinking about it, given that Dracula's already known as practically the master of evil, it's difficult to imagine any secrets he has being darker than what he's already known for, which does lead one to wonder if these secrets are of a rather different nature...
In Castlevania: Portrait of Ruin, Death appears out of nowhere to block Jonathan's attack on the newly-risen Dracula, and the two fight you together. When you KO one, Death gives Dracula his power and Dracula uses Power of Dominance to "merge" Death's soul to his and become True Dracula. Soulmates...?
In Castlevania Judgment, after defeating himself in a Mirror Match, Death opinions that "One advisor is all the Master requires." And his ending sequence: "Death, unconstrained by mortality, pursued every possible means of reviving his master. Why would such a being serve Dracula so loyally? Perhaps there is some greater force at play behind it all..."
In Judgment, Carmilla is referred to as "Dracula's plaything" by Alucard, and one of her victory lines implies that only Dracula can satisfy her. (Poor Laura.) And yet she remains jealous of how Death is "always at Dracula's side".
In Castlevania: Harmony of Dissonance, Dracula will use a different cry at the beginning of his boss battle if you engage him as Alucard. "Come, my son; let us embrace!" Because that isn't awkward or disturbing at all...
In Castlevania Dawn of Sorrow, Dmitri implies that Genya wants to protect Soma at least in part due to affection he still harbors for Dracula.
In the radio drama "Nocturne of Recollection," there are serious ho yay vibes between Alucard and Lyudmil with lines like, Lyudmil: "Master Alucard, I will always be here, forever… somewhere close to your heart." and Lyudmil: "Once a year, the youths would make a garland with these flowers and present them to young girls to express their love." Alucard: "This wasn’t mentioned in Mother’s diary…" Lyudmil: "Since we are here, why not let me teach you how to make a garland." Alucard: "No need." Lyudmil: "I see…" There's also mild ho yay between Alexis and Cyril, and between Magnus and Lyudmil/Alucard but that's hardly a surprise considering Magnus is an incubus.
Isaac, the villain in Castlevania: Curse of Darkness, has a modest amount of Foe Yay with protagonist Hector, but his one scene with Trevor Belmont is just full of it, with Isaac driving Trevor's own dagger through Trevor's body, pressing up against him, whispering in his ear and kissing him on the neck before "pulling out". It gets worse if you consider that Isaac may be possessed by Dracula at this time. Foe-threeway-yay? My head hurts.
The first thing Dracula says when he is revived in Belmont Legacy comic is "Belmont! You are mine!". And his (naked) resurrection, which immediately precedes that line, is intercut with said Belmont and his new bride consummating their marriage.
Hugh and Nathan of Castlevania: Circle of the Moon are rivalslash-tastic - when your happily married straight male friend announces that Hugh has it bad for Nathan and the subtext is far too large for the Gameboy screen to contain, you know you are not simply seeing things. Dracula is rather - something at Morris Baldwin, too.
Cave Story has the infamous scene that implies an Optional Sexual Encounter between the player character and Chako, a female mimiga... somehow. In Curly Mode for WiiWare and Steam, where the player controls Curly Brace instead, the scene plays out exactly the same way.
Telly Vision from Chibi Robo seems awfully dedicated to Chibi, even vowing to "rebuild Chibi from [his] own parts" the first time Chibi faints from lack of energy.
Glenn: Cyrus, wait! I... I...! CYRUUUUUUS! Cyrus: My heart burns with my memories of you...
In Crackdown, your contact in the Agency seems a little too pleased with how well you're... "developing".
Darksiders has a fairly squicky example with the Watcher. Not only does the guy set a new standard for JerkassExposition Fairy, he invariably treats War like his bitch. Seriously, half his lines sound pretty kinky even IN context.
I always knew you had it in you.
Watch out, or I'll really get under your skin.
In Darkstalkers when Morrigan was absorbing a dying Lilith into her being (Lilith isone-third of Morrigan's soul that was sealed away and then took on human form) they have quite the suggestive pose, especially given they're both are Horny Devils that wear Stripperific outfits.
Mondo and Ishimaru "battling" it out in a sauna to see who will last the longest. The next day, they become almost too close. Then Ishimaru doesn't believe that Mondo could ever kill anyone, even after he confessed. He then goes crazy after Mondo dies, creating Ishida.
Aoi and Sakura seem to have some Les Yay going on.
Hitomi and Lei Fang in the Xtreme spinoffs appear to be very fond of one another.
In Xtreme Beach Volleyball, you can give gifts to the other girls to raise their friendship meters, and they will often gift you things back, such as bathing suits from their own personal collection. The bathing suit that Lei Fang gives Hitomi when her friendship level hits max? A white bandeau bikini with red polka dot trim that says "LOVERS <3" in red glittery cursive. Lei Fang will NOT give this to anyone else you play as; it's the same style bathing suit, but it's plain yellow with no text on it.
Destroy All Humans!: Crypto and Orthopox tend to sound like an old married couple. In one moment of unsual giddiness, Pox calls Crypto a "silver stud."
Dante and Nero from Devil May Cry. The first fight they have, when Nero meets Dante after Dante shoots Sanctus, Nero flies into the air, and straddles Dante's waist, and Nero bites Dante's 'gun'. Whenever the two meet back up with each other during the game, it almost seems like Dante is flirting with Nero.
Part the first had Argilla gaining an instantly fast rapport with Jinana, a rival tribe leader, the two having conversations about "Sadness" - having only been recently awakened to emotions. When she dies, she calls Argilla "Comrade", a very emotionally charged word in their world. Later on, while Argilla bawls her eyes out, Heat sarcastically calls Jinana "Argilla's Girlfriend". Bat talking about devouring Jinana acts as Argilla's Berserk Button.
Lupa is the one who got Gale to awaken to his emotions. And in the second game, Gale sheds some of his Straw Vulcan tendencies, espousing the other man's honor code.
The Foe Yay of Heat/Serph can be brushed off as competition over Sera for a while... until Serph and Sera merge into a single hermaphroditic being... and Heat comments that he/she's "cute". Well, that's one way to resolve a love triangle...
There is quite a bit between Axel and his director in Disgaea 2.
After Mao ambushes Almaz and mugs him of his (wannabe) Hero title in Disgaea 3 he wastes almost no time in drafting the poor guy as his lab rat, and takes a rather strange fascination towards him from that point on (particularly over that his new pet can teach him about this "love" thing). The Master/Slave overtones just snowball from there.
Almaz: Uh... I think I've just been violated.
In Disgaea Infinite, but Mao does it again, with Laharl (debatably, almost all of his conversation with Laharl is made with a flirtatious tone).
Mao:You're too good to be true! I must capture and examine you~!* huff* * huff ** drool*
Disgaea 4 continues the "tradition" with Fenrich's devotion to his lord. Fuka speculates that Fenfen is jealous of Artina and and one point asks him "if he swings that way". She doesn't get an answer, sadly.
Fenrich's affection for Valvatorez is questioned in Dimensions 2 by Etna if she stands right next to him in battle. She describes it as "That type of relationship" similar to how she describes Adell and Rozalin's relationship causing him to lash out at her personally, but not denying the relationship they share is more than just one of trust.
If you max out his affection with anyone, he is very quick to deny any feelings for Valvatorez... yet the problem with that is all he talks about when you max out his affection is his Lord and when talking to Valvatorez, he states that Val can use his body for whatever he wishes.
In the Fuka & Desco Show, during one of the Eyecatches, Fuka ends up knocking Valvatorez over. Fenrich catches him, and this◊ happens.
The song "Naked Requiem" played at the end of Tyrant Valvatorez mode seems to be sung from the point of view of Fenrich. It also has some... suggestive lyrics.
In the Netherbattle Tournament, Tyrant Valvatorez tells Fenrich that he was conjured up by his desires, which Tyrant Val claims is his desire for him to win the tournament and rule the Netherworld. However, based on Fenrich's dialogue and sprite, it's clear that he desired something else from Tyrant Val.
Create a Android, and it mentions Val/Fen slash. Yes.
With the Legendary Tree, you can set any two characters as "lovers". Yes,anytwo. This will get you a cutscene where they hold hands and give each other loving looks.
There's definitely a lot of Les Yay between Fuka and Desco, especially on Desco's end with her being as loyal to her Big Sis as Fenrich is to Val. This◊ happens in one of the On the Next segments. During the Flonne segment of the post-game stories, both Fuka and Desco briefly suffer Mind Control and are obsessed with spreading love to everyone. When they snap out of it, Emizel says he was worried that Fuka was really confessing love to him. Desco says that had better not be the case because "Big Sis belongs to Desco!"
Create an Alraune and you get a cutscene where "she" is speaking to a crowd of adoring fans. Another character shows up to announce that the Alraune's educational background is fabricated, because it consists entirely of girls' schools... and the Alraune is actually a guy! The crowd doesn't care, and admits they "don't mind a little trap action" as long as "she's" cute.
The Alraune convict in Hades is so impressed with the characters' deeds, that she insists one of them date her. Any of them.
In the hybrid board game/RPG Dokapon Kingdom, the heroes, regardless of gender, are competing for the Princess' hand in marriage. At the end of the game, if a girl wins, the King objects - though the Princess says she really doesn't mind. The King then dons a wedding dress and offers to marry you instead, as he wants a bloodline. This doesn't go over very well, and the final shot of the game seems to imply that the Princess and her heroine went through with the marriage anyway.
In Dragon Quest Heroes Rocket Slime, Hooly's mother, as with all the captive slimes, sends a letter when rescued. In it she mentions that Hooly "Sends his lo... says hi." Though, with her tendency to embaress him, it may simply be poor wording on her part.
Yaha, one of the guardians of the Districts, openly admits at least three times during the boss fight that in the past, he had a crush on Urick, a former member of the Knights of the Seal, and that he made his pact with the gnomes in order to win Urick's love once and for all. But Urick rejected him. So now Yaha is sad. And really campy. Ironically, during the boss fight Yaha insinuates that Urick returned his feelings before Yaha made the pact.
Urick and Nowe seem far too friendly in their dialogue for just old friends. Direct your attention, if you will, towards Urick's death scene, where Nowe holds Urick in his arms as Urick lies there dying, and then lovingly deposits his body in the funeral pyre of the burning Holy Flowers.
Zhang He gets progressively campier with each entry. In Dynasty Warriors 6, he flirtatiously taunts his opponent "You've come alone. Was it my beauty that drew you?" Given that 80% of the playable characters are male, the odds that this line will result in Foe Yay are very high. Tended to originally be paired with Wei strategist Sima Yi (even after Sima Yi kills Cao Cao and usurps Wei in 6), but in 6 there were hintings of an attraction to Xiahou Yuan, while in 7 he's just campy and flamboyant without attraction hinted towards anyone (other than a platonic affection for Xiahou Yuan).
One of the games ends with Sun Ce and Zhou Yu riding off into the sunset together.
Ling Tong and Gan Ning have too many moments to count. There's one battle in particular in Dynasty Warriors 6 where if you kill one half of the pair, the other is consumed by Unstoppable Rage. Incidentally, this is exactly the same reaction you get from Lu Bu when you kill his canon Love Interest Diao Chan. They're all but canon in Ling Tong's ending in Dynasty Warriors 6 Special, especially in their final scene together.
In DW: Empires 4, one of the unlockable endings had Sun Quan lovingly stroking Zhou Tai's face... pissed as a fart, naturally.
Mitsuhide gets a lot of Ho Yay, not only with Ranmaru in Samurai Warriors, but also with Nobunaga Oda, of all people, in SW2 and Motochika Chousokabe in SW3.
And in the Dynasty Warriors: Gundam series, you get the unexpected Gundam crossoverHo Yay. For example, playing as Domon Kasshu, rescuing Seabook Arno, and hearing him dreamily inform you that "My soul has drawn you here... or at least, that is what I want to believe." Domon is also fond of informing characters like Heero Yuy and Kamille Bidan "Anyone who gets in our way will taste the power of our passion!" Your... passion, hrm?
Earth 2150 gives us a quick joke about this kind of thing: during one Mission Briefing of the Neo Campaign in the original game (playing LC and deciding to join with the ED) Neo mentions that in the case of Fang's superior not going with his methods, he will release videos of her making out with a girl from the info department. She is understandably very angry about that.
Rei and Miku clearly care deeply for one another. And often in VERY sexy lingerie in many of their scenes together. That Rei is still mourning her husband might or might not add to this.
When it comes to Ho Yay, Fatal Frame 2 is the undisputed champion of the series, with a healthy dose of Twincest on the side. A pair of identical twins, aged anywhere from young children to older teens, are forced to perform a ritual in which one twin must kill the other in order to become "one". It does not help that the one time the ritual is seen performed, it can easily be interpreted as having sexual overtones.
There is a lot of Les Yay, some of which goes beyond subtext - see its page for examples.
One incident in which Shirou fails to realize that suddenly telling his (male) friend to take his clothes off is... kind of weird. Issei blushes a lot, and Shirou has to strip him by force. A lot of Issei's normal behavior could qualify.
In the second scenario, U.B.W., the designated sleazy brat, Matou Shinji, expresses a fair amount of attraction to Archer.
While Issei had a great deal of Ho Yay already in Fate/stay night, Fate/hollow ataraxia manages to top that by making it hard to deny he has a crush on Shirou.
Hana and Rain from Fear Effect: Retro Helix, which played up the quasi-lesbian subtext between the two characters for all it was worth. It's all but confirmed by the last half of the game, and the cancelled Fear Effect Inferno would have had a Love Triangle develop between Glas, Hana, and Rain, while Rain and Deke would have become girlfriend and boyfriend. Talk about fun relationships!
In Fist of the North Star: Ken's Rage, Jagi and Amiba have a very odd relationship, just look at the ending FMV for them, they both have each other's arms around their waists. I'm sure it wasn't intended to look so gay, but it does.
At one point, Jagi asks Amiba, mid-mission, what is it with him and musclebound guys. It was probably very intended.
In Fossil Fighters: Champions, Pauline is hinted to have a crush on the main character... regardless of their Purely Aesthetic Gender. Even if you play as a girl, she'll blush when she's forced to hold hands with you, and when she looks deeply into your eyes, she wonders why she can't bear to look away.
In Fragile Dreams: Farewell Ruins of the Moon, Crow and Seto kiss. Seto is surprised, but doesn't show anything to prove that he disliked the kiss. Crow kissed him because he never had a friend before, and he thought friends kiss on the lips, but the scene was still cute. It'll break your heart once you see Crow's death, and that Seto embraces him until he dies.
Freddi Fish has some of this between Boss and Spongehead, who hold fins for a bit.
God of War has Deimos, Kratos' brother; check the original GOW at the end of the credit's theme, as well as the main trailer for GOW: Ghost of Sparta.
Isaac and Garet were very close, but nothing too suggestive. By Dark Dawn, the two had moved into a cabin in the mountains together to raise their sons. With the boys' mothers nowhere to be seen.
In the first game, Babi, the ruler of Tolbi, had a very loyal second-in-command named Iodem.
In Dark Dawn, Amiti's easily-offended attitude toward Eoleo tends to be read as Tsundere by the fandom.
Also in Dark Dawn, when setting off from Belinsk after triggering the Grave Eclipse, Sveta is quite rightfully depressed, having seemingly lost everything she loves. By the next morning, she seems to have recovered, and when asked about her remarkably quick turnaround, she gets evasive and starts blushing. Seeing as how Karis made the boys sleep out on the deck while she and Sveta took the cabin...
Amoretta and Lillet's relationship in Grim Grimoire is full of this. Amoretta's first meeting with Lillet seems to show her developing an outright girl crush on the heroine, which includes her saying the line, "I like your smile. Can I touch it?" and Lillet nervously agreeing to it. It's explicitly established that Amoretta lives because of Lillet's love sustaining her (it's complicated), and Amoretta's deaths are more devastating to Lillet than any of the others. They do wind up together near the End Game... sort of. And they live together in the post game epilogue.
Nearly every single one of May's win quotes against a female opponent involves her commenting quite visibly on how attractive they are. She says it's about evaluating their worthiness for Johnny, but it's not exactly hard to instead read her as a closeted lesbian who's trying to convince herself that's why she keeps noticing this.
Sol Badguy and Ky Kiske definitely have some Ho Yay going on. They often appear a bit too close in official art, and in "Accent Core" their entrance pose, they're practically kissing.
Waify Bishōnen Endrance unambiguously falls in love with the main character Haseo, simply because the heroes needed his help. In-game mails suggest that Endrance's player is pansexual. He was similarly dependant on Mia back when he was Elk, and his affections as Endrance transferred to Haseo after the cat on his shoulder (referred to as Mia) turned out to be AIDA and was destroyed.
Ovan's apparent obsession with Haseo is more than a little creepy.
The same can be said about Bo's great admiration for Haseo (and Haseo's strange kindness towards Bo, seeing how Haseo was a Jackass to everybody when he met Bo).
In Friends of Mineral Town, if you show the Blue Feather to Grey, he blushes and says something about not liking those sorts of things.
In the Japanese version of Cute, you can "Best Friend" one of the special girls. They have the same lines as in the DS version, you have all the same events (you can even give them chocolate on "Spring Thanksgiving"), you "best friend" them, and you have a child together. In the same game, the Mineral Town girls are extremely affectionate to you, and constantly mention the fact that you "play" together.
In More Friends of Mineral Town, the girls accidentally mention girls if you show them the Blue Feather. They also act the same as they do in Friends of Mineral Towns, so once you become friends with them they really do seem to have a crush on you.
In Harvest Moon Frantic Farming, Foe Yay is blatant between the Witch Princess and Harvest Goddess, with bickering like a Tsundere couple, and, in the final chapter of Mark's story, they blush at the thought of working together, while protesting that they don't actually want to. This may be intended to be blushing over Mark... but it doesn't really come across this way.
In his route, Kazuaki has a marked-out photo in his wallet that he explains is somebirdy he loved who left him. From the context, this was assumed to be a love interest, possibly a wife. Then it turns out in the "Bad Boys Love" route that the bird who left him was Nageki, his foster-brother.
Yuuya overhears Sakuya talking about him, and replies along the lines of "Well, now the boys are into me, too?" (Note: Sakuya is his brother.) The add-on manga and drama CDs say that Yuuya gets gifts of birdseed from lots of other students on the bird equivalent of Valentine's Day. They also spell out that St. Pigeonation's is a boys' school (with one exception).
After meeting the biker-girl sparrow Azami and getting rescued from a gang of thugs by her, the heroine announces that she's in love. Azami isn't a possible love interest.
Louis is following Kyle around like a lost puppy and is nearly brought to tears of rage when you insult him or withhold information.
Louie's backstory involved leaving Manhattan with his best friend Danny; the way he talks about it, it's like they were going to elope and find some place to settle down together and raise their kids away from the ugliness of the city or something.
IF is a Chick Magnet who has the attention of RED, Vert, and 5pb. Hyperdimension Neptunia mk2 has IF almost kissing Nepgear just to let Nepgear transfer to Purple Sister. It's one of the first few CGs you unlock in the game.
Neptune would sleep with Compa and hug her to the point IF lampshades what the hell she's looking at.
Hyperdimension Neptunia Victory refers to the Relationship Values between every pair of playable characters as lily point (subtle). And then there's Iris Heart, a woman who thinks Noire looks 'cute' with a pained, teary expression that apparently makes her look like she "just became an adult", and politely asks a villain to wait so she can basically put her friends through an S&M begging routine before handing over the artifacts that would save everyone's lives.
As if being a Chick Magnet isn't enough, Yuri also has some subtext with a few other male characters. The most notable one is with The Rival Cico, who gets furious when he thinks Yuri broke his promise to go to LMC together with him. Even when they meet again ten years later, he doesn't seem to lose his obsession to Yuri. His line of dialogue before they settle their score doesn't help.
Cico: Ha ha! Now there's the Yuri I know and love!
Torlo occasionally calls Yuri as "my man". Sure, it is probably his way of calling him "buddy" or something like that, but still...
Dietrich really respects Yuri and seems happy whenever he is assigned under Yuri's command, even going so far pleading him to accept the proposal to lead the battle in Adis, just so he can fight alongside his fleet. Right before his death, he apologizes to Yuri for unable to keep his words to stay alive, and Yuri seems to be shocked upon hearing his death.
Official artwork shows Izuna and her traveling companion Shino in very close proximity of each other. In-game, however, Izuna merely thinks of Shino as a sisterly figure.
The sequel first introduces Shino's younger sister Shizune, who instantly takes a strong liking to Izuna - when they meet, she gives her a no-holds-barred glomp, complete with boob-squishing. If the two are in a dungeon together and you initiate a Tag Attack with Izuna in the lead, Shizune will float up to her and kiss her face (the screen sillhouettes, so you can't exactly tell where), with hearts floating up the whole time. This fully recovers both girls' HP. Then there are the times when Shino ends up Brainwashed and Crazy, and it's implied that Izuna would go after her before anything else, even if Shino wasn't conveniently waiting at the source of the problem. Shino herself has a line about how she'd never choose between Izuna and Shizune if anything happened. (OT 3, anyone?) This isn't even mentioning things like the Furo Scene, where Suiren rests her head on Fuuka's breasts as if it's no big deal... These games' stories are big on girl power, but damn.
Jak and Daxter have this at times. One notable scene is when an incredibly inebriated Daxter hugs Jak while slurring "I love you, man!" (Which earns a disturbed look from Jak.)
Kenji has a habit of being far too familiar with Hisao, including confronting him in the bathroom while both of them are naked, which coupled with his misogynistic rantings makes it appear that he has a crush on Hisao. The Act 1 ending, in which the two of them share a "manly picnic" together, is generally known as "the gay ending" for this reason.
Lilly and Hanako are... very close. It's repeatedly established that for years Lilly was Hanako's only friend, Hanako almost idolises Lilly, Lilly displays a level of comforting warmth around Hanako that far surpasses the motherly/big sisterly instincts she does around other students, and they even get a Sleep Cute moment on a train. To top it off, during Lilly's route when Lilly explains to Hanako that she and Hisao are in a relationship, Hanako delivers a speech that screamsI Want My Beloved to Be Happy (granted, it could theoretically be directed at Hisao, but the two barely interact in Lilly's route).
Shizune and Misha are almost literally attached at the hip, Hisao continually being surprised when he sees one without the other, with both of them giving him a "we are separate people" line (as if it's a comment they receive frequently). Shizune's route is more about the relationship between the three of them rather than Shizune and Hisao's relationship specifically, to Threesome Subtext levels. It turns out Misha does have feelings for Shizune and confessed a while ago, but Shizune doesn't return her feelings.
Emi seems genuinely hurt when Hisao mentions that Rin said she doesn't consider Emi a friend, mentions that the two of them had shared a bed on occasion, and Emi helps Rin out with certain things that Rin's lack of arms would make difficult—such as changing her tampons and washing hard-to-reach places in the shower.
Nurse makes a lot of borderline - and some past borderline - flirtacious remarks to Hisao. He says he's joking, but Hisao doesn't find it funny.
A very Stripperiffic Exchange lieutenant on the Citadel Station hits on the protagonist during her involvement in a sidequest, and she does so regardless of player gender.
There is some Ho Yay between Male Exile and Atton, during the light side dialogue options when you turn him into a Jedi. Paraphrasing, "Think of when you wanted to protect me, how you felt when I was in danger." And the references to them playing strip pazzak.
The Last Remnant: In addition to the bartender in Athlum (a blatantly obvious example of this trope) there is also some significant Ho Yay subtext between Rush (the protagonist) and David (the Marquis of Athlum).
Laura Bow: The Colonel's Bequest has Laura snooping around the mansion looking for clues to the murder mystery. If Laura enters the french maid Fifi's room at a certain time, Fifi changes clothes and Laura will spend some of her time watching her undress.
In The Dagger of Amon Ra Laura gets blatantly hit on by a woman in a speakeasy restroom, and ends up changing clothes in front of her. During a long sequence of eavesdropping on all the museum offices, it's possible to find out that the flirtatious Yvette is just as happy to canoodle with women as she is with men.
In Left 4 Dead 2 there's a function on Xbox 360 where you say the person's name your cross hair is over if you press and hold down the left analog stick. Ellis tends to say Nick's name very... sensually, with a certain amount of what can only be described as lust, more times than he says his name normally. Ellis goes through trauma whenever a survivor dies, but especially when it's Nick. Here's the paragraph on them from the Left 4 Dead Wiki:
Nick insults Ellis and makes fun of him on several occasions, but this seems to be more of a "joke" between the two of them. Ellis even seems to look up to Nick a bit, starting conversations with him such as having the same suit or sometimes being excited at Nick shooting the helicopter pilot. Nick, for his part, will compliment Ellis's shooting or ask him if the Midnight Riders are any good, which may be an attempt to bond with him. Though it may seem that Nick is less caring towards the younger man, he has a soft side too, like if both survivors (Coach and Rochelle) are dead, or if Ellis is dead he will sometimes apologize for his behavior. Ellis is always sad to see Nick die. However, Ellis is also angered by Nick when talking about horses, in the sense that Nick has a like of horse meat, and Ellis states that "horses are for riding" and not meant to be eaten. He also may sometimes call the Spitter "Nick's Mom!" Ellis does still see Nick as a very good friend, as in "The Passing", he may suggest that he and Nick get a tattoo with "Bros" on it, and will respond to Nick's exclamation of "I hate you Ellis," with "well I like you, Nick." Though Nick is rough around the edges, he seems to care for Ellis more then he comes across like (sometimes) if he heals Ellis he says things like "Don't tell the others this, but I'm doing this for you."
Ellis exhibits Ho Yay-worthy quotes on two more occasions. When talking about Jimmy Gibbs Jr. ("If the laws of nature would have it, I would bear that man's children"), and when Rochelle jokes about 'someone' having a crush on that 'awesome biker dude' ("Well I don't doubt it. That is a cool guy!")
Kain and Raziel from Legacy of Kain. From the opening of the first game, to the way they become insanely obsessed with one another, to the way they finally make up at the end of defiance, with Raziel healing Kain's heart. There's also Kain/Moebius, Moebius/Elder God, Elder God/Raziel, Raziel/Janos Audron, the list goes on. The following piece of dialogue is infamous:
Raziel: How is it that you know my name? We have never met. Moebius: On the contrary, Raziel - I know you very well... And it grieves me to see how cruelly Kain has used you. I knew you when you were one of the Sarafan brotherhood, Raziel. We were even close.
In the Kirby games where you can do Face-to-Face, a returning ability which allows you to heal your teammates immediately after eating a health item by touching them, in-game it can look like Kirby's kissing his teammates, who are all male.
Dart: Huff huff huff! Lavitz: This is the second time you saved my life. Dart: Huff, huff, I was just around. Lavitz: Even though that was the case, I was lucky you were around, Dart. It'll be a long relationship we will have.
Dart: Yup. That's right. Shana: Excuse me, you guys! Don't leave me like that!
Even the least slash-inclined player is bound to raise an eyebrow at Avin and Mile in Legend of Heroes IV: A Tear of Vermillion.
The Legend of Zelda: Ocarina of Time, with Link and the Poe Collector; the first time he encounters Link he says: "Oh...you are quite an energetic young man. You're brave and handsome, too... Heh heh heh...your name is Link, isn't it? Heh heh heh...don't be surprised. I can read people's minds. If I looked as good as you, I could run a different kind of business...heh heh heh..."
Sheik: It is something that grows over time... a true friendship. A feeling in the heart that becomes even stronger through time...The passion of friendship will soon blossom into a righteous power through it, you'll know which way to go...
Twilight Princess: After her life was saved by her (temporary) Heroic Sacrifice, Midna was noticeably a bit too intimate when it came to Princess Zelda...since they didshare a body for quite some time... This seemed to be returned by Zelda, since in the final scene she appears to be even more disappointed than Link that Midna is leaving forever.
In the Oracle of Seasons manga, Ricky the kangaroo was quite Gay for Link: gushing over the Chosen Hero, oozing admiration at Link's sword skills, and openly voicing his disappointment at the possibility of him having a female love interest... Ricky having a pouch makes this one questionable.
The Legend of Zelda: Skyward Sword: Given some of her dialogue/behavior, as well as how fiercely protective and devoted she is toward Zelda, it can make one a little curious as to the exact nature of the relationship between Impa and Hylia before the events of the game.
The Legend of Zelda: The Wind Waker has Carlov the sculptor. After you get the color picto box, you can give him pictures and get figurines that give you information on any character, enemy, or boss (always at least one tidbit the rest of the game doesn't tell you.) Well, if you take a picture of figurine enthusiast Manny (the guy who hangs around the gallery) and give it to him, though he's excited about any subject you give him, he'll gush about this one in a way that's very hard to see as platonic. "That golden, freshly brushed hair... That stylish, yet unassuming bod... Why, this is a mighty handsome man! Mercy! My very soul compels me to make a figurine from this picture!" Oh, and the official art of him is holding a figurine. Of who? Yes, Manny. (Carlov gushes even more about the subject's beauty if you take a picture of Carlov himself, though; he seemingly doesn't recognize the picture as himself.)
Atsuki and any guy character. Special mention goes to Akira, whose Character Development comes from his interaction with Atsuki. If you talk to Ryo in the final chapter of the Bad Ending, he'll say something like "I think it'd be great if we could always be together— Oh, wait, did that sound weird? Like a proposal or something?"
During Shinji's Gaiden scene, picking the right options and encouraging him to follow his dream of being a doctor will cause him to blush and respond with something like 'Geez, trying to be cool... Not like I care what you think, but...' And then he smiles. '... Thanks anyway.'
Yui and Mako. You won't go so far to snap at everyone and tries to avenge the one who kills your partner if you're not that close.
The relationship between Hibiki and Ryo, childhood friends who do seem really close; nurse Suzu even fantasizes about their relationship (although she does the same with female school nurse Honoka and practically adopted son/younger brother Hibiki: 'A forbidden teacher x student romance!'). There's an archive scene dedicated to their relationship which while focusing on Ryo and his new co-worker, you see another side of Hibiki that you don't see in the game.
Picking a certain answer while talking to Suzu will cause her to include Atsuki in her little daydreams, and Hibiki does take an immediate interest in Atsuki, even causing the students around them to stop and look when he accousts Atsuki in the hallway. After Hibiki loses his psychic abilities, he seems to have formed an even stronger bond with Atsuki, if his final words ('So, you're leaving, then? ... No, you don't have to answer that.') are any indication.
Riki and Kyousuke straddle the line between this and canon – at one point in the VN, Riki outright admits he has a bit of a crush on Kyousuke, but it never comes up again and Kyousuke's feelings are only implied, and in the anime it's ambiguous on both sides.
Riki and Kyousuke could have a whole page to themselves, but to sum up the important bits: a huge theme of the game is of them Holding Hands, which they do quite oftennote Yes, it's because of the idea of leading someone by the hand, but the game is definitely well aware of the ho yay involved – see Mio's happy sigh when Riki confirms that Kyousuke always used to take his hand when they were little, they're very touchy to the point where Mio honestly thought they were going out at one point, Kyousuke says at one point that he doesn't mind sharing an Indirect Kiss with Riki, and in general Riki's fawning commentary (to the point of saying he totally understands why girls stare at Kyousuke while he reads manga because he looks 'divine') edges into 'schoolboy crush' territory pretty regularly... And then there's the scene where, in response to Masato asking Kyousuke who he likes, he responds 'right now, Riki is my number one', causing Riki to become very flustered (and in the anime, when Riki says he doesn't like him, Kyousuke becomes really depressed), or the scene near the end of Refrain where before Kyousuke disappears, he and Riki end up yelling at each other passionately that they like each other and wish they could spend their whole lives together, using the exact same words they would use if they were confessing their love. And in the end, not only is there a lot of evidence supporting it, there's absolutely nothing in the game that contradicts the idea of the two of them being in love, ether. And this is still just the beginning!
Riki and Masato. Multiple times Masato acts jealous when Riki shows interest in someone else, and while he says it's just because he won't be able to hang out with Riki as much, Riki instinctively interprets it as romantic jealousy. And one of the losing titles Kengo can give to Riki is 'In a love triangle between Masato and Kyousuke'...
Les Yay between Haruka and Rin when Rin unexpectedly compliments Haruka, who is so pleased she starts staring after her and wondering whether what she's feeling is love. And we can't forget that time Komari worried that, since Riki saw her panties, she would never be able to get a bride (not be one, get one), either...
Magician's Quest (Enchanted Folk for those of you in Europe). You can get people of the same sex to say that being with you creates a "sense of meaning", and it offers an equivalent of the "Declare Love" incantation for the same sex to promote "Best Friends". Also, if you visit the Limelight with one of your friends, you'll get the same analyses regardless of the gender of your friend. Mentions of "significant others" abound!
In Mana Khemia: Alchemists of Al-Revis the main character Vayne Aurelius and Roxis Rosenkrantz have a good deal of Foe Yay going on. Even Roxis's ending is Ho Yay-tastic, with Vayne and Roxis becoming sparring partners (ahem), and the loser then subjected to the winner's experiments. It all sounds kind of kinky. By the third character quest it was outright Ho Yay. Vayne's tone of voice in Japanese in Pamela's third character quest when it concerned Roxis is hilarious to listen to ("But... Roxis...!"). Among the items you can alchemize are collars, for Sulphur. For one of them, Roxis snarks at Vayne as usual but mentions aside that he thinks putting a collar on Vayne isn't a bad idea (granted it's supposed to be more of a controlling a rival thing but if that doesn't sound questionable, what does).
Pepperoni and Goto are uncomfortably chummy with each other, and there's a line somewhere around the game about how they will "ride on each other". Chapter 3 of Pepperoni's character quest has him practically scream in ecstasy when he oil wrestled Gato. In Chapter 4 of Gato's character quest he had to pretend to be attracted to Pepperoni and Enna to break up with Marta. Enna was constantly disgusted by the whole ordeal, Pepperoni on the other hand enjoyed everything.
Of all people who become the target of her incantations, Chloe is really fond of using her childhood friend Ulrika as her guinea pig.
Yun and Raze, especially in later chapters. The ending where Raze is hired to become his adoptive daughter's bodyguard doesn't help, since practically that makes Corona has two daddies.
Luigi and Prince Peasley in Mario & Luigi: Superstar Saga. What with Peasley giving Luigi a rose for easy access to the castle ("It suits your green") and Luigi practically twirling with delight! Yeah, and there's also that business with Luigi blushing when Peasley strikes him with a sword upon acceptance of a bet. Prince Peasley seems to interact more with Luigi overall for sure...
In Marvel Ultimate Alliance, Doctor Doom and Loki are interestingly familiar with one another, calling each other "my good doctor" or "my friend", not to mention that Loki seems to be getting pretty annoyed with Doom keeping another magic user, Baron Mordo, around the castle. Then there's the fact that they screw over Baron Mordo and Ultron and leave to take Odin's powers together.
Zero and Axl become very friendly very fast. Or at least, Axl does. He seems intent on barging in on subtext-filled scenes between X and Zero for much interruptions, leading to a little pocket of the fandom to joke about his block powers.
In one ending on Mega Man X8, Zero says "Maybe I won't have to fight anymore..." then smiles and looks towards X as if he was imagining something.
When X and Zero reunited in X6, Zero had a small blush on his face.
The dialogue between Geo and Pat in Mega Man Star Force is filled with this, especially during the Gemini Spark chapter. It continues in the sequel where, in the Apollo Flame quest, Mega Man destroys the alternate version of Gemini Spark and is actually worried about Pat, unlike the other fights, where he doesn't care less about the bosses that were merged with his friends in his dimension, not even Sonia, the very first friend he made with who is arguably the closest person to him, herself. It's made even worse by the Viewer Gender Confusion.
Metroid Prime 3: Corruption has Gandrayda, a female shapeshifter, blatantly hit on Samus multiple times ("Thanks, Sammy.", "You really shouldn't trust strangers, Sammy. This is going to be fun."). One of Gandrayda's attacks is an "atomic glomp" - she jumps at her target and throws her arms around their neck, irradiating the hell out of them, looking very much like she's about to kiss them. The subtext gets worse if you notice where the glomp move puts the rest of her body, especially when she pulls the same move on Samus, depicted in first-person. Samus seemed to take Gandrayda's death a bit harder than the other hunters she was forced to kill.
Several comments made by Tony to his best friend Jeff seem to point to a good deal of one-sided subtext. He also gives Jeff quite the extended phone call ("Is this Jeff? Oh happy day!"). Shigesato Itoi confirmed it as canon.
That guy guarding the Mani Mani statue at Sidemoon, and when you show him the guy with the golden tooth, both of them leave to go get a drink.
Porky's slightly creepy obsession with all things Ness and Earthbound-related probably isn't just because he's homesick.
While underwater, you must fill up on oxygen by kissing robot O2 tanks who look like middle aged mermen wearing bright red lipstick. When you do it makes your whole party blush. In the last part of the game there's a centaur version that offers oxygen above water for no reason. During the underwater stage one of the Pig Masks comments that he kind of likes them, disturbing his comrade.
A Pigmask nervously offers you an item when you're dressed as "the commander" and insists it's just a friendly gift.
There's something fishy about how exactly Ionia showed Lucas how to use PSI.
Flinty-poo ~<3 ...What? That was my Magypsy impression. Do you like it? ...Don't act so embarrassed!
In Neverwinter Nights: Hordes of the Underdark'': During the Valsharess's last offer for you to join her before she sends her forces in an attempt to destroy you, if you are playing a female character there is a lot of lesbian subtext being thrown about. She especially gets mad if you tell her that you aren't her type.
In No More Heroes Travis accidentally sends a recording of himself humping a pillow back to the video store. What is on the pillow? A burly masked wrestler. And the Samurai-esque relationship he has with his master Thunder Ryu, with all its shudo implications. And given that Thunder Ryu makes sure that Travis keeps his ass clean for some of the techniques he teaches him...
Due to the Purely Aesthetic Gender rule, many examples are present in the first game if the social leader is a female, for example, Deneb will compliment the player's good looks even if they are female, and if spared, the towns people will say you did it because she was a pretty girl. Another boss claims the social leader is jealous of his skills with women.
If Junpei enters Door 5, then examines the bed multiple times, Snake will comment on it.
Snake: Junpei, I cannot help but notice your interest in the bed. Perhaps you are hoping we will spend time on it, together...
Junpei: Gah! Y-You—! I— Don't say stuff like...damn! That's not a mental image I want!
In the Safe Ending, Snake's death is one of only two deaths in any of the bad endings that causes Junpei to completely flip his shit, to the point that he has to be physically restrained, then punched in the gut and carried out by Seven to keep him from running to Snake and locking himself in the incinerator. The only other character whose death has ever evoked that kind of extreme reaction is June, Junpei's childhood friend and love interest.
Pajama Sam 3 has this too in the ending montage where General Beetfoot is seen giving Carrot a flower while the latter smiles bashfully.
Parappa The Rapper: Parappa's "best friend", PJ Berri, assists him in the second stage of PtR2, entitled Romantic Love. The clincher? Parappa and PJ do more together "romantically" in this one stage than he does with Sunny Funny in two whole games!
Tatsuya Suou and Jun Kurosu: Jun definitely thinks of Tatsuya as more then a friend, whether or not the player has Tatsuya reciprocate his feelings. The game itself and some interviews would lead us to believe that Suou and Kurosu are the intended pairing. The drama CD "Errors of Their Youth" practically operates on the assumption that they're dating.
Tthe rather questionable devotion that King Leo has for his boss, Joker-sama, in which at one point during Innocent Sin he describes the Joker as being "as beautiful as a goddess" under the mask. Eternal Punishment only adds stalkerish tendencies on Sudou Leo's part.
There's some hints at sexual tension between your character and Aria. The game features Purely Aesthetic Gender, meaning that if you pick the girl character at the beginning, Aria's dialogue is exactly the same.
This dynamic is reversed in Shadows. Keith's lines are already filled with romantic subtext, so playing as a boy invokes the trope.
If you play as a boy, some of the actions and dialogue of your rival apply. Likewise, some of the dialogue from FireRed/LeafGreen if you play as Leaf◊, the female protagonist, due to dialogue not being changed.
There's one little bit of the massive Pokémon section where some think that, since Erika and Sabrina's Pokémon having some Psychic and Grass moves respectively in the Stadium games, it implies subtle Les Yay.
If you play as Dawn you get a considerable amount of Les Yay with Cynthia. If you play as Lucas, you get Ho Yay with Barry (and ambiguous Foe Yay with Cyrus).
In Pokémon Black and White, you get to go on a ferris wheel with NPCs that vary with the season and which gender you chose. The conversations on these rides are loaded with Ship Tease. If you play as the girl, one of your potential partners is a waitress. As the guy, you get a male hiker. You also go on the ferris wheel with N... Even when you're playing as a male.
GLaDOS harbours a level of obsession for Chell that is suspect even for an insane AI that can apparently think of nothing besides Science and Cake. While being a monumental Unreliable Expositor makes it difficult to know when she's being sincere, she really does seem regretful about trying to kill Chell (it being part of the testing procedure) and her unexpected retaliation. The ending song (sung by GLaDOS) includes the line "I'm not even angry / I'm being so sincere right now / Even though you broke my heart and killed me...". When Chell breaks the first morality core the subtitles say that GLaDOS's voice gets less mechanical and "more seductive", but she sounds flirty even before that ("Despite your violent behavior, the only thing you've managed to break so far... is my heart.").
Portal 2 is far, far more blatant, wavering between Tsundere and full-blown Psycho Lesbian territory. GLaDOS seems entirely convinced that Chell attacking and "killing" her was without any justification and is furious at her "betrayal", attempting to guilt-trip her constantly with lines that are variations of either "how could you do that to me?" or "now you'll never leave me". Then, when a power-mad Wheatley becomes a threat to them both they actually grow to become friends, relying on and trusting each other, although while eventually GLaDOS decides she doesn't want to kill Chell, that doesn't mean she wants her around. This culminates in "Want You Gone", a break-up song in everything but name, and provides even more evidence that GLaDOS is a massive Tsundere. (For extra points, the final line is deleted from the subtitles, reading only as [REDACTED].)
My beautiful dear, my darling beauty! My li’l girl, oh Chell! That she holds her in such esteem! That she holds her in such esteem! Oh my beloved, fare thee well! My dear child... why dost thou not stay further away? Yes, away from Science! My dear, dear baby... Ah, my beauty! Ah, my dear! Ah, my dear! Ah, my li’l girl! Oh my dearest one!
The relationship between Layton and his apprentice, Luke, is seen by some as having... undertones. Batman and Robin-like undertones.
Layton and his friend Clark are pretty affectionate in the ending credits of the fourth game.
There's a ridiculous amount of chemistry between Layton and Descole - the latter bends the former over a control panel in the Movie! Even more disturbing in context when you find out that Descole is Layton's brother.
It's almost harder not to see Kiel as having a thing for Stocke. At one point when Raynie and Marco are teasing him for his crush on Field Marshall Viola, he admits (after saying that one of the things he looks up to her for is her beauty) that there is one person he admires more than her. The only thing anyone is surprised about when he admits that he's talking about Stocke is that Kiel actually said it straight out.
Ambiguously GaySpace Pirate Rusty Pete from the Future series is quite blatantly obsessed with Captain Slag, crying over Slag's decapitated head and having it talk to him like a ventriloquist dummy, saying things like "You may not have me body, but you will always have me heart". He eventually rewires Slag's head so it can talk again and calls it "Slag on a Stick", and later attaches it to the decapitated body of Angstrom Darkwater to revive him.
Ratchet and Clank themselves. They're certainly very close friends, and have probably lived together through all of the 'between game' periods. Both of them have had multiple love interests, none of which ended up being more than hinted at before mysteriously vanishing for the next game. In the Future series, the normally cheerful Ratchet tends to have a bit of a breakdown when Clank goes missing. And Clank risks the universe in order to undo Ratchet's death in A Crack in Time.
How about Wesker and Chris? It becomes increasingly obvious that Wesker has a blatant crush on Chris. And their incredibly blaring Ho Yay/Foe Yay gets a lot worse in Resident Evil 5. Wesker takes every opportunity to scream Chris' name in the most dramatic way possible, and has the obvious tendency to ignore everyone except Chris. Also, the incredibly hot Excella, who was coming on to him like crazy, only receives contempt and annoyance. However, as soon as she mentioned "Chris," he actually smiles, and she wonders if the sudden expression means he's "concerned." Chris has a female partner during the game, whom Wesker largely ignores in favor of going after Chris specifically. And it's not just because he has a history with Chris - he also largely ignores Jill during the fight at the Spencer mansion. Jill was just as responsible for ruining Wesker's plans as Chris was. And all this is not even mentioning the final battle, where Wesker ends up shirtless in tight leather pants, and continually uses his tentacles to grapple with and molest Chris. Oh, and how about Wesker's furious anguish when Chris leaves him to die by escaping on the helicopter? "CHRIIIIIIIISSSSSSSS!!" This ends with Chris shooting him with a rocket launcher, telling him to "suck on this, Wesker."
They have plenty of Ho Yay in "The Umbrella Chronicles" too. In pretty much every scenario where you can play as Wesker, Wesker mentions Chris and how he looks forward to the next time they meet. Oh, and during the Wesker scenario "Dark Legacy" Wesker is eavesdropping on Chris and Jill as they discuss their plans to take out the final Umbrella facility in Russia. Wesker is also going there to steal some research and he says, "Chris, it appears our fates are forever intertwined."
Birkin acts like Wesker just broke up with him in Umbrella Chronicles/Resident Evil Zero. The whole scene was him trying to convince Wesker to not leave Umbrella because he still wanted to stick around and finish his G-virus and then completely flipping a shit when Wesker still wanted to leave. They were research partners for at least 20 years, starting when their mentor attempted to encourage a rivalry between them but accidentally sparked an instant bond which other scientists comment on, complete with nicknames... and even at his most unstable and paranoid, the almost cartoonishly-insane Birkin will listen to and trust Wesker... well, these things add up. Especially when they go on their version of a date - killing their boss, stealing his research and taking over his lab.
Resident Evil Revelations has Parker and Raymond, with Parker taking a bullet for Raymond and them saving each others' lives, and Parker nicknaming Raymond.
Leon and Buddy in Resident Evil: Damnation. Despite their initial antagonism, the two of them bond very quickly at the end, even fighting in perfect tandem. Buddy practically kills himself to manipulate the lickers into saving Leon from the Tyrants, and Leon is unable to leave him at the mercy of the Tyrants and therefore risking his own life.
Resident Evil 6 introduces a new character for Chris to be with: Piers Nivans. While every other male character has a female lead to possibly ship with, Chris only has a male partner. From his "Yes, Captain!" to his jalousy of Finn receiving Chris's attention, he is often thought of as Chris's personal powerbottom.
Rune Factory 3 has Carlos, big brother to one of the potential brides of the game. Although he claims that all the ladies love him, he comes on to the main character in a variety of ways.
If you befriend the townsfolk and then don't speak to them for a while, talking to them will trigger a "Hey, long time no see" dialogue. Carlos' is "Have you been avoiding me? Not cool, bro!", while Rusk gets a pouty/angry face and dialogue which really only seems appropriate for potential love interests. Then consider most of his 'quests' are just giving you sweets...
The Boss becomes awfully fond of Shaundi, even if the Boss happens to be female. The second-to-last mission in The Third, ends with the Boss having to choose between hunting down Killbane and rescuing Shaundi from a monument that's been rigged with a bomb. If the Boss chooses to go after Killbane, Shaundi dies, and that's considered part of the Bad Ending.
A female boss has several Les Yay moments with Kinzie and Kinzie herself with Viola. There's also Ho Yay between a Male Boss and Gat or Pierce.
Sam & Max: Freelance Police has this is a good amount. This is even Lampshaded in the series several times. They have been mistaken for a couple more than twice, Sybil, the psychiatrist, found their perfect match as each other, Sam insists that "[Max] doesn't even like girls", as well as the fact that Sam goes into either unstoppable rage or deep depression if he thinks that Max is dead. They definitely are, however, Heterosexual Life-Partners.
Sanada Yukimura has some of this with Mitsunari, Keiji, and Kanetsugu.
Oda Nobunaga With Ranmaru. Lines likethis only add fuel to the fire. This is inspired by their historical connection.
Akechi Mitsuhide's relationship with Ranmaru in SW 1 could only be more explicit if it were a hentai game. Come SW 2, it shifts to him and Nobunaga, with some Foe Yay elements.
In SW 3, he has this with Motochika instead. The subtext is so heavy it might as well just be text. The XL expansion and Empires game have him refer to Mitsuhide as his 'soulmate' several times! Motochika also said that Gracia, Mitsuhide's daughter, is like a daughter to him, too!
Hanbei with Kanbei. Likely inspired by their close historical relationship.
Despite being married, Muneshige seems very fond of Kiyomasa. Many of the things he says to him could be considered very flirty indeed. He also teases Mitsunari quite a bit.
Kanetsugu with Mitsunari. Especially with scenes such as this! Also with Keiji, Yukimura, and Masamune in SW3.
Okuni's various endings in SW1 have her going home with different warriors as escorts, and one of these warriors is Nohime! She flirts with plenty of ladies in SW2 and Warriors Orochi as well.
In Sengoku Basara 3, in Motonari's stage while playing as Mitsunari, he will refer to Mitsunari's "lover's spat" with Ieyasu.
In Shadow Hearts: Covenant the amount of sheer homoeroticism between Joachim and his mentor, the Great Gama, is so intense that the other characters are rather creeped out. Except for the little girl, who instead gets starry-eyed when things reach their logical conclusion. Joachim does flat-out state that he is gay if you choose him during the torture sequence. The Great Gama, meanwhile... is twice as eager.
Roger in Shikigami no Shiro III gets intensely jealous of Kohtaro's shikigami, Sayo, and loathes the fact that she gets to spend so much time around his "beloved Kohtaro".
In Shin Megami Tensei III: Nocturne, there is a male junk shop owning Manikin who loves to flirt with the protagonist, who is also male. The junk shop Manikin is extremely flamboyant, and says 'fabulous' a lot, calls the protagonist a cute little boy, hot stuff, handsome, and tells him that he hopes they will have a long-lasting relationship, and then winks at him (though if you talk to him in Ikebukuro, he will reveal he has been Mistaken for Gay and is slightly insulted by being mistaken for a "queer", though he could be Armored Closet Gay). The Collector Manikin and the Protagonist have a tiny bit of Ho Yay, you need to squint to see it. The interaction between the two is just REALLY cute.
Shinobido brings us the twin sisters Ageha and Usuba, who leads a gang of all female ninjas and are strongly implied to be lesbians (judging on their... weird discussion about Usuba's faked breasts (for a disguise).
It might seem odd to mention The Sims 2, a game best known for its Everyone Is Bi mechanics. However, the stories of the pre-packaged characters are uniformly straight, except for Strangetown's Pascal Curious and Nervous Subject. True, the game opens on them as friends, but Nervous is coded to walk by the Curious household just as Pascal goes into labor with his alien baby. There is also a pretty big chance of Nervous autonomously making a move on Pascal, even tough the latter is straight, which would usually stop male sims from hitting on him.
In Sonic Heroes, Shadow, who has no memory at this point discusses Sonic's "date with Eggman" as a "date to die for" with a ravenous smirk. Sonic appears to flirt with Shadow in Shadow the Hedgehog. Some people cite Knuckles weird tag-alongs with Sonic despite his duty to the Master Emerald and some of his stranger dialog as being evidence of Sonic/Knuckles as well.
In thisSoul Calibur 4Omake, Cassandra is is a little too interested in destroying Hilde's clothes... She is also very excited to show Hilde's her new revealing outfit (and at the same time pressures her to try cosplaying). At another point she poses in an even more revealing outfit and asks "...want to play with me?". This can be interpreted as being addressed to the reader or Hilde. Cassandra also gets very upset at discovering that Hilde has a "partner".
Tira's Critical Finisher in the game itself. It's a death kiss. Which can be performed. On anyone. Even women.
Soul Calibur V has a smattering of Les Yay here and there; one of the most obvious is the Romantic Two-Girl Friendship between Xianghua's daughter Lexia and Taki's student Natsu, but the one most plot critical is Pyrrha's status as a Replacement Goldfish for Tira. Not only does the girl inherit the extremely abusive Foe Yay between Tira and Sophitia, but gets to grow up isolated and paranoid because of Tira's Yandere tendency to kill anyone that makes her happy so that Pyrrha will never trust anyone but Tira and become a new host for Soul Edge. Since Tira has been working this plan since Pyrrha was about three, she not only manipulated and lead to the death of Sophitia for Soul Edge's purposes, she went on to perform Wife Husbandry on her daughter.
In Star Control II, Admiral ZEX is quite obviously lusting after the Captain. It is suggested that you don't think about that. Given that ZEX's attraction is a bit... different from most examples on this page, you could also call this a case of Mars Needs Men.
Star Fox 1 has its share of mild homo-eroticism hints - usually in the forms of various awkward dialog localizations (like how Wolf has a tendency to act gay towards Fox). This is somewhat parodied in Super Smash Bros. Brawl, in a communication link with Wolf. Leon gushes in orgasmic jealousy about how vicious and efficient Wolf tears into his enemies, and Panther, in a fit of confused disgust, has to ask him who he's in fact jealous of: Wolf, or his victims.
In a rarely seen Private Action, Claude and Chris from Star Ocean: The Second Story have some Clone Yay when they meet outside a bar and Chris offers to buy Claude a drink. Fop that he is, Chris is thrilled as beans to be drinking in a prole bar with someone and thanks Claude for the companionship... and then gives him a friendship ring, albeit one that boosts stats. (One guesses it does so through The Power of Love.)
Albel and Fayt in Star Ocean Till The End Of Time, where a requirement for making Albel join your party is to say that you "don't hate him"; in their paired ending, the two resemble an arguing couple. And the manga where the two are paired in awkward situations.
Nel and Clair have heaps of Les Yay, ranging from a hugging scene to Nel saying "I did it, Clair!" when she levels up. In the ending, Clair gets irritated when her father Adray tries to marry her off to men, saying that she'll "find her own husband, thank you very much".
While it's not nearly as blatent as Fayt and Albel, Fayt and Cliff definitely show signs of a Bodyguard Crush for a good chunk of Elicoor.
In First Departure, Millie and Mavelle (Marvel in the Japanese version) get some mostly-one-sided Les Yay. Millie, upon being asked about Mavelle, immediately goes into how beautiful she is and how she just had to ask her to join her and Ronyx (Ronixis). And when you first see Mavelle in Ionis, Millie almost throws herself at Mavelle while complaining that she was afraid Mavelle was going to get herself killed and that she shouldn't worry Millie like that.
Star Ocean The Last Hope has a good deal too, even if it gets buried under the canon pairings most of the time. There's Edge's one-sided rivalry with Crowe, Edge's attempts to talk Arumat into getting life extending treatments on EN II so that his genetic enhancements won't prematurely end his life— he even tries to kiss him, albeit jokingly. And Faize's adulation toward Edge. His feelings toward Edge actually play a big part in the catalyst for his Face-Heel Turn—he doesn't start hiding things from the party until his faith in Edge is shaken. The end is particularly rife with this, as well. Edge is the only one besides Lymle to figure out who the Apostle of Creation is, and is the first to run to him when he collapses after the he's defeated. He then stays behind to help Faize, and falls after him when he lets go of Edge's hand instead of just cutting his losses and going to his friends. Their conversations here and before the final battle are quite emotional.
In the Star Trek: Elite Force game, your character, Alex Munro, slowly falls for one of the other team members, Telsia Murphy over the course of the game. Par for the course, right? But then you remember that you can choose the gender of your character at the beginning of the game... and all the cutscene dialogue stays exactly the same, regardless of gender.
Quite a bit of Les Yay can crop up between Luna and Venus in Steambot Chronicles: Battle Tournament. It's probably not just an artifact of Purely Aesthetic Gender, either — the game is voice-acted, so they would have had a fairly good incentive to remove the Les Yay lines if they'd wanted to.
Heavily implied between Ryu & Ken throughout the whole series, especially manga and anime. Ken has repeatedly joined these Tournaments to see and or fight Ryu, though he's married with a wife and son.
There's some implications between Gulie, another married man, & Charlie. Even after the events of Street Fighter II, where Bison dies a vicious death at the hands of Akuma's ShunGokuSatsu, Gulie still seeks out any and all Shadowloo activity.
In Street Fighter IV, Sakura's winning quote against Sagat indicates she sees him as a romantic rival regarding Ryu.
Pretty much every game in the series has this. If it's not the close friends like Flik and Viktor (though Flik had a girl in Suikoden I, he was still traveling with Viktor in Suikoden II and were mentioned as still traveling together in the 15 years between II and Suikoden III) then there's the Narcissists - every game has two or three frumpy males (and in some cases females) who very loudly proclaim their close 'friendship' for each other.
In Suikoden III, Cecile comes across as having a fawning girl-crush on Chris. And Chris having a Furo Scene where she notices that another girl is covered with scars — why she spends the entire scene staring at the other girl in order to notice just how scarred she is isn't discussed.
Chris and Yun, especially in the manga.
Lucretia, the protagonists' strategist in Suikoden V is almost explicitly stated to be bisexual, with possible romantic links to both Lelei, the woman who once guarded her prison cell, and Cathari, a sniper who may have once had a contract on her life, as well as a prior husband. And then there's the prison guard's Furo Scene... (And Lelei and Lucretia are heavily implied to spend the night together before the final battle. In the Where Are They Now ending credits, it turns out Lucretia left the country without telling anyone, except Lelei, who went with her.)
There's a pretty amusing bit towards the end of Suikoden Tierkreis where Asad, who has quite clearly had a thing for Lady of War Chrodechild throughout the game, ponders who the biggest obstacle in his way of his affections is. At first he thought it was her Number Two Meruvis, but changes his mind to Fredegund... which would be incestuousLes Yay. Whether or not the subtext was deliberate or not, it really does not help that Fredegund gets very gushy around her sister.
The hero has quite a number of subtext with other male characters, and that's not even consdiering the others.
Sugar, a female water spirit from Swordcraft Story, has been sworn to marry the person to whom she's bonded. If you choose Pratty as your main character (a female), she responds with the following line when Sugar offers her a kiss: "No no! I, uh, kiss other girls all the time!", and that's only the initial meeting. For extra points, Atlus put that screenshot on the back of the box.
Varil has... undertones with a male PC, especially when Varil's butler states that 'all Master Varil was missing was you.' And prior to that, Varil's out-of-nowhere demand that Cleru's Guardian Beast stay behind. After the Ariel and Mariel match, Varil ping-pongs from 'You were nowhere near as strong as when you beat me!' to "Is it because they're girls? Or do you have a crush on them? Which one is it?" to 'Well, I guess I can understand.' Cleru is absolutely lost. Varil tells him it's okay, then compliments Cleru's style.
Varil: "Girls have to be protected." What beautiful words. You sound like such a gentleman... Anyway, that's how men should behave. Varil: [his ending] With you by my side, Cleru, Craftlord of Iron, we'll make it for sure.
The sequel features a lot of Les Yay if you choose to play as a female, mostly thanks to very lesbian Lovable Sex Maniac Lynn.
Given that most lines are identical regardless of if you choose a Male or Female characters, otherwise innocuous scenes - such as BFFRyougablushing and getting flustered during the intro and ending segments, or Orin (who, for extra effect, is your Adopted Older Brother) doing the same or comforting you - becomes Ho Yay-tastic. Same goes for Gabriel, particularly his ending, and maybe Arno depending on how you see it.
Angel!Dinah tries to get a kiss from the player character, no matter what their gender is.
Rai and Ryusei, made all the more obvious to the point of it becoming a Running Gag in some of the comics by the way Ryusei is not interested in girls (only mecha).
Excellen is a walking font of Les Yay. She might be Kyosuke's canonical love interest, but doesn't stop her flirting. She even admits to wanting to bone Viletta at one point!
Lemon Browning, Excellen's alternate universe counterpart, is hooked up with Axel, but gets very loving around Lamia, even when they are enemies. Lamia even calls her Mistress.
Certain members of the Chimera unit, but that's more or less canon.
The Project T.D team's female members. It's strongest between Ibis Douglas and Irui Ganeden, the goddess who is the villian of Super Robot Wars Alpha 2. They have a unique ending scene where they meet in an empty space after Ibis fails to save Irui from the destruction of her unit. Irui comforts her for her failure and tells her not to cry before teleporting Ibis to safety and dying.
Bian Zoldark and Maier von Branstein, an older version of the obvious Ho Yay dynamic between Ryusei Date and Radiese F. Branstein.
Gilliam Yeager occasionally gets drawn into the Sanger/Elzam Ho Yay jokes. The only Aggressor immune to this is Kai.
It's obvious Katze Kotolnos thinks Haken Browning is a hot piece of ass.
Shine and Latooni get depicted this way in some official art, with Latooni having a blindingly obvious crush on Shine, though Shine has an obvious crush on Rai. Latooni is at first reluctant to wear a cute dress but changes her mind when Shine compliments her on it.
Syu seems to be more bemused than pissed off by Masaki. In a way, Syu could be getting off on the aggression, and purposely riles Masaki up to keep it going. Considering he hangs around a very perverted Dark Action Girl (and is not ungrateful for her company), it possible this is his kink (it's hers too, but it's probably more subtle in Syu's case). In the ending of Lord of Elemental in his route, Syu ends up blushing brightly when he sees Masaki in just bathing trunks.
Archibald has a creepy way of pissing off Rai and Elzam that carries some overtones of this.
The freeware adventure game Sweet Dreams. You play as Amy, who has to rescue her friend Juliet from her own dream world. In this dream world, Amy is somewhat inexplicably thrust into the role of the Prince who has the wake the sleeping Princess Juliet. When you finally reach Juliet, you're given the option to wake her with a kiss. And then, as part of getting her to wake up from her dream, Amy tells her that "You'll always be a princess to me."
Another early Hanako Games title Summer Schoolgirls is a giant flaming mass of playable Les Yay. Given that the credits include a thank-you to the Shoujo Ai community, this is completely intentional.
Various other Hanako Games tend to include varying degrees of Les Yay... and prior to creating Hanako Games, the creator behind it released a few Interactive Fiction works under the name Papillon, several of which go straight past Les Yay into "explicitly contains lesbian relationships."
An awful lot of the lines Heavy says to Medic are pretty homoerotic sounding, whether intentionally or not ("GET BEHIND ME, DOCTOR!", "I LOVE THIS DOCTOR!" etc). Considering that the Medic and the Heavy are best paired together as a "tank and healer" deal, it's possible that this was completely intentional.
One of Sniper's achievement is "Beaux and Arrow", in which you have to kill a Heavy & Medic pair with the Huntsman. While beaux can technically mean a frequent and attentive male companion (which Heavy most certainly is with Medic), it's most commonly associated with boyfriend, lover, sweetheart and other such terms.
In "Meet the Medic", there's an awful lot of contact going on, even taking into account the Doc's less than sterling bedside manner. Forget all the metaphors; just the fact that Heavy's willing to be the Doc's personal guinea-pig says a lot.
In the Love and War Update Scout got a new weapon called "The Back Scatter" and new achievements, one of them is called "Back 2 back" in which Scout has to use such gun and kill a Heavy and Medic pair within 20 seconds of each other. The achievement icon is a broken Heart Symbol.
If you look directly at the Medic and call him, the command is different. For example, instead calling "MEDIC!" Heavy will say "IT'S TEAM TIME DOCTOR!" The Soldier will say stuff like "C'mere sister", "C'mere pumpkin", and ultimate Ho Yay"C'mere Sweetheart..." Not even Sniper escapes it; it's like everyone is gay for medic.
The Heavy, being a Boisterous Bruiser with a poor understanding of English, has lots of lines like this. Consider his "THANKS FOR THE RIDE!" response after being teleported by an Engineer.
The line the Spy gives when he dominates an enemy Spy: "See you in hell, you handsome rogue." Admittedly, all Spies look exactly alike, so this may be more of a case of Self Yay.
Both the Heavy and the Soldier can equip a 'Pocket Medic', a small doll of the Medic carried in one of their pockets. The Medic even has an item called the Gentleman's Ushanka - a hat similar to one of the hats for the Heavy. Its description reads, "[This] hat makes the perfect complement to the Officer's Ushanka. Let the officer in your life know you'll always be right behind them, with a Medigun at the ready and a matching wardrobe."
The Sniper and the Engineer can equip a small pocket Spy doll named The Itsy Bitsy Spyer. The description is : "Is that a miniature spy in your pocket or are just happy to OH GOD STOP HITTING ME!"
The Soldier and Demoman were close friends in the comics, they'd rather die than kill each other but they are tricked into fighting.
Possibly the strongest relationship in the game is between Arawn and Pwyll, from their first meeting - rife with Manly Tears and Meaningful Handshake and exchanging True Names - to the moment of Arawn's first 'death', and then the multiple times that Pwyll manifests in the present day. They go from being potential enemies to Heterosexual Life-Partners in about fifteen minutes, and there's a lot of mentioning of 'walking the same path' and 'our city/cities', and watching them with Primula comes off like she has two daddies: Arawn's "Geez... Pwyll, is raising a child really this hard?" and Pwyll understanding what Primula was saying about learning the Ancient Magic. Arawn was absolutely adorable after Pwyll explained that whole 'friendship' thing, and Pwyll's internal monologue...
Pwyll Voiceover: That's right... He was a fallen angel. The same blaze that condemned me was the same that had mercilessly condemned him. He threw himself into that fire, burned away his brilliant white form, and dyed himself in darkness. And he was still burning in that inner fire even as he stood before me. ... His ice-cold eyes met mine directly, condemned me, and called to me. Saying... 'Fall with me.' So... So I...
Later it's Arawn and Arthur, who's near-identical to Pwyll but with a different personality. They're Back-to-Back Badasses in the anime's opening sequence, while eating an apple (though they make a point of obscuring just what part of the apple Arthur took a bite from); when Arawn nearly dies again Arthur snaps him out of dying (though Arawn briefly hallucinates Arthur as Pwyll); then there's the scene in the Avalon courtyard, during which time Arawn's voice is softer than we've ever heard it before (while speaking to Pwyll's ghost and when calling Arthur back inside). Oh, and when Arthur reclaims the sword Danwyn, Arawn's half of the matched pair starts glowing and humming like a cellphone in your back pocket. Played with during the tournament (game-only) when the party is split into opposing teams; Arthur and Arawn are on the same team, Arthur's sister Rhiannon is on the other, and before the fight Rhiannon accuses her Oniisama of 'stealing her time with Arawn-sama!' while the other girls query why, if Arawn got to choose the teams, they aren't on his team (though Arthur is).
Between Arthur and Spoony BardTaliesin, as well as one-sided hero-worship for Gaius from his subordinate Decimus; the former involves Taliesin commenting that Arthur can't die because Taliesin 'has prior claim on his life', while the latter is made more obvious in the anime (and possibly the PS3 game).
In the anime, Gaius's almost suggestive tone while talking about building a 'freer, more tolerant world,' and Decimus' reaction, seem to be implying a tolerance beyond freedom from theocratic rule.
There's a copious amount of Les Yay from Octavia and Morgan, who are also Back-to-Back Badasses at multiple points; Octavia also gives Morgan a 'friendship necklace,' and they hold hands during the seige of Avalon. Then there's the Les Yay and/or Foe Yay between Octavia and former roommate Lydia...
Test Drive Unlimited shows what might be the laziest Les Yay in the history of creation: all PC characters and NPC characters get the same animations for the two kinds of hitchhiker missions - in the "Hitchhiker" missions, the dude asks for a lift, you give it, and he thanks you and leaves, and in the "Top Model" missions, the babe asks for a lift, you give it, and she thanks you, flirts with you, and leaves. Take this Double Standard, add the option for choosing a female PC, and... well, yeah.
The FlanderizedPlucky Comic Relief versions of Larson and Pierre, seen in Chronicles, are inseperable for the first two levels, and Pierre inexplicably offers to buy Larson a milkshake.
The Crystal Dynamics trilogy is rife with Les Yay, mostly of the Foe Yay variety. Lara and Amanda particularly come across as having had a really bitter breakup in Underworld.
In the 2013 reboot, if Lara and Sam were explicitly stated to be a couple absolutely nothing about their relationship would have to change. Sam calls Lara "sweetie", constantly fawns over her, and trusts and defers to her unconditionally at all times, while saving Sam remains Lara's primary motivation for much of the game, with the final levels being straight out of a Rescue Romance. The ending manages to top this by them leaving the island with Lara bridal carrying Sam, while Sam is wearing a white dress.
Sam: You saved me... I knew you would. Lara: I made you a promise.
Adel and Derek in the third Trauma Center game. It's not really there at first, but then there's a situation where Adel gets sick, and someone else besides Derek does the operation. When Adel finds out, he acts like Derek just left him at the altar.
Vitriolic Best Buds Shiki and Arihiko never use Honorifics to address each other, but what makes even Shiki's own sister do a Double Take is Shiki's habit of referring to Arihiko by his first name (a habit usually attributed to girls). Shiki having a similarly put-upon, what-the-hell-are-you-thinking- idiot demeanor in his Slap-Slap-Kiss relationship with Arcueid also helps.
In the sequel Melty Blood, the villain that changed the main character into a Vampire Refugee also killed her best friend; a Church Knight named Riesbyfe. She crafts a bullet out of Riesbyfe's artifact, and in the manga kisses it before using it to kill the villain. In a sequel, a different villain manifests Riesbyfe as a spirit program. After beating the villain, Sion uses her magic to keep up the manifestation, and while holding Riesbyfe in her arms◊; tells her "you belong to me, now."
There are few couples in later games like Will/Lion and Erika/Dlanor.
Author somewhat likes making lots of Ronove/Battler fanservice in TIPS and Ougon.
Vagrant Story is a game where the cast is almost entirely male, and most of them walk around in skin-tight borderline fetish outfits (the main character wears assless chaps, and he's not even the only one). Half the dialogue has some kind of homoerotic subtext, with Sydney/Ashley, Sydney/Hardin, Ashley/Guildenstern, and Jan/Sydney (though that's quite onesided. Poor Rosencrantz). But cult leader and primary antagonist Sydney Losstarot deserves special mention here. He's all but outright stated to be bisexual, described by Agent Merlose as being so beautiful and charismatic that his followers give their bodies as well as their souls to him. Every single one of Sydney's dialogues is positively dripping with blatant sexual innuendo, particularly his scenes with Ashley. Rosencrantz is another Launcher of a Thousand Ships, albeit to a lesser extent, since he has Belligerent Sexual Tension with half the male cast. Guildenstern inexplicably calls him a "harlot" of all things, and he has a significant Clingy Jealous Girl moment once he realizes Sydney has chosen Ashley to be his successor instead. Cue Jan's What's He Got That I Ain't Got?! speech.
Engineer Dallas Wyatt has "Man Hater" and "Fancies Women" as character traits, and most (if not all) of her quotes relate to main heroine Alicia Melchiott in some way.
Jann Walker is a makeup wearing man who loves other men, especially Largo.
Isara's the one Rosie acts most Tsundere to (she was never as tsun-tsun to Zaka or the other Darcsens), Isara's the one who get Rosie's deredere side out and it was Rosie who was hit hardest by Isara's death. Rosie's song, A Love Passed On, was specifically promised to and first sung for Isara.
Quite of few things that Russell can say ends up with Nate responding in some sort of flirty manner, intentional or not. From the beginning to end, Nate can possibly come across as being very "friendly". If Russell doesn't hide from Nate and tells him that he needs a ride, Nate will respond by asking if he'll work for it because he has "needs", though he'll soon say that he was joking. When in the car if Russell asks Nate if they can just drive instead of talk, Nate responds with confusion over the plural usage and asks if Russell wants to sit on his lap. He apologizes soon after for freaking him out. At the gas station when they're both getting shot at, if Russell responds with fear, Nate will ask Russell to look at him. If Russell refuses, Nate will cup his chin, not so roughly make Russell look at him, and motivate him to continue on. With all of these moments from Nate and the more friendly actions on Russell's part - accepting the drink, apologizing for being scared, thanking/acknowledging that Nate saves his life when he falls, and staying with him at the end - it can make this part of the game seem like a slash fic.
In Season 2, Luke and Nick have a few moments like this. Kenny comments on this when trying to get a rise out of them.
The intro trailer for Warhammer Online trailer contains some relatively subtle Les Yay (that probably counts as Foe Yay) between the nameless High Elf Shadow Warrior and the Dark Elf Sorceress.
At one point in WET, Rubi visits a lady by the name of Kafka Dvorak, who's into ancient books and who she wants info from concerning Mr. Ackers. Kafka seems to have something of the hots for Rubi, considering the way she acts toward her during their first meeting, and the fact that she practically feels her up suggests that she might have a bit more than just a crush on Rubi (this being Kafka, who knows what she really wants to do to her?). The mission you go on for her is called "Falling for Kafka."
In Wild ARMs 2, Brad Evans and Billy Pilder are incredibly close-knit former war comrades who maintain a deep emotional attachment to each other long after Billy has stopped fighting. Their interaction is usually of a deeply sentimental variety, with the brain-injured wheelchair-bound Billy known to keep calling out Brad's name, while Brad is periodically shown to be keeping Billy firmly in his thoughts and feelings. In Japan they're together, and the game's English translation didn't cover that up very well.
In A Witch's Tale Princess Gretel responds to discovering that Liddell (a young girl herself) rescued her by saying "Both strong and lovely, you must be sent from heaven" while a heart appears in her character portrait. She later comments on how she knows she can trust Liddell because she has "pure eyes", with the heart appearing again.
Sorceress Philippa Eilhart's relationship with her apprentice Cynthia borders on a Running Gag in The Witcher 2: Assassins of Kings, where Geralt keeps hearing moans from behind their door, only to walk in on something other than the obvious - first time Cynthia giving a sensual massage to Philippa, the second Philippa giving a sensual whipping to Cynthia; gives her official title "leashed sorceress" a completely new meaning. There's also discussion with Cynthia where she expresses admiration to the lifelike illusions Philippa is capable of doing, most notably a garden where "the fruit and she-elves are juicy".
Odd example for a game where the player characters have no personality comes from Wizardry VI: Bane Of The Cosmic Forge. At the end of the game, if you choose the peaceful method, you confront the vampiress Rebecca and have the option to tell her that you love her, regardless of the party member speaking (who can be male or female). She gives that character the Diamond Ring, the best defensive trinket in the game or its sequel. The kicker? It's only usable by a female character. Hmmm...
Joshua seems uncommonly interested in Neku, and tries to get the two of them to travel the streets alone during his chapter. Sure, he has a reason for it that's important to the plot, but the voice he uses makes him sound outright flirtatious. In the manga, Joshua is stalking Neku, and takes a picture of his ass with his phone. Lampshaded in the omake chapter "Another Day: This Day Ends with You!":
Joshua: Hello, Neku. How long the days have felt without you.
While pitching the Red Skull pin all over Shibuya with a cry of "Come and get some hot stuff!", Futoshi slowly and sensually backs into Makoto as the latter grins the entire time. If the player builds up his Friendship Gauge at Shadow Ramen, he thinks you're coming onto him. "This isn't in the manual!" During week 2, he calls the Prince 'baby', and when some issues pop up during one of their 'business conversations' Josh gleefully remarks there seems to be 'trouble in paradise'. Oh Ai, poor dear, you never had a chance.
The assistant in Wild Boar in Udagawa. When you get his FSG up high enough, he acts like a lovestruck schoolgirl, thinking such things as "(Don't go!)"
The flirtatious shopkeeper in Cadoi City. It sounds like fairly typical male-to-female come-ons at first, but when you think about it, the only consistent party member (and thus, the only one he can be addressing, given that his lines never change except in response to increased friendship) is Neku.
That little chat between Joshua and Neku in regards to Minamimoto...
Joshua: Think he's got a thing for you, Neku? Neku: What?! How the hell do you figure that? Joshua: Oh please! The way he follows you around?
For some Les Yay, Eri really misses Shiki, Uzuki idolizes Konishi, and Ai doesn't seem that devastated when she explains to Mina that her date with Makoto ended up kinda sucking.
In the Xenosaga games, there's a very strong, definitely intentional element of Les Yay between Shion, and KOS-MOS, the beautiful robot she designed. It doesn't hurt that the fetish level of KOS-MOS's outfits depends directly on how much Shion has to do with that body's design...