Persona 3/Ho Yay

Ho Yay involving Male MC
The Hero (Minato) is pretty much the game's Launcher of a Thousand Ships.
 * This Troper sees a hell of a lot between Minato and Akihiko too. Hell, Minato and the majority of the male leads have more likely pairings than the main female leads at times.
 * Pharos is so obviously crushing on Minato, it gets vaguely squicky. I mean, the only times they talk are when Minato is in bed, and Pharos is sitting on the end of the bed in what looks like pajamas...which is visibly reminiscent of the other times the Social Link is sitting on the bed.
 * Tanaka and The Hero, played for Squick.
 * Says you.
 * His threat to post a picture of you on a dating site for convicts also suggests they'd find Minato pretty cute.
 * The Main Character and Akinari, the Dying Young Man.
 * And don't forget Minato and Ryoji, which is the most popular Ho Yay ship in P3 for Japan.
 * Episode Luck Seems to be hinting Minato/Ryoji
 * In the female path of the game, Ryoji reveals that he would like you even if you were a boy.
 * Speaking of social links, French exchange student Bebe (Temperance) is quite affectionate toward the main character, to the point of waiting outside his classroom in the higher levels of the link. Not to mention that his plot, which revolves around, can be read as a metaphor for coming out.
 * Not to mention him and the protagonist having a "delectable time" when they went to the candy shop after their first Fashion Club meeting together.
 * The Lets Play plays this for laughs, with the Main Character having a very blatant guy-crush on Bebe.
 * Kenji Tomochika (the Magician/Classmate Social Link) giving the protagonist a choker at the end of his Social Link because 'he doesn't look fashionable enough'.
 * Surprisingly, there's some between Shinjiro and the Main Character. The former often expresses his concern for the latter's health, especially after the MC recovers from his cold in September. In one of the Drama CDs, Shinji even makes food for him while the MC's sick.

Les Yay involving Female MC

 * Aigis acts exactly the same as she does in the original even when you play as a female. She is also the only female character who will privately see FeMC off in a tender moment during the ending.
 * In the her 8th and 9th social rank, Aigis goes through something that looks suspiciously like Gayngst. And confesses to the female character at that!
 * Aigis's feelings are barely even subtext -- I mean, what else could the thing she wants in relation to the protagonist that she can never have because she's neither human nor male possibly be? And the max rank event has heavy sexual overtones as well. She takes the MC to her room, asks her to touch her intimate inner, uh, robotic workings, and then you get the "you spent a long time with Aigis" message with fade to black...
 * Mitsuru asks the female protagonist to hold her hand while watching a scary movie.
 * She even asks the FeMC to live with her during her Rank 9 event, after asking her to run away with her during rank 8.
 * Way back, in the beginning of the game, right after you fight the first Shadow, you'll meet with Yukari again before going to school. If you've act nice to her up until that point, she'll blush as she says your given name for the first time.
 * That doesn't even begin to cover it. A lot of the links for the FeMCare subtext-riffic. Her Hermit Link, Saori, could easily be read as having a crush on her. A lot of the holdover 'romantic' links have... interesting vibes too, like with FeMC/Fuuka- the Max event has the two of you baking a cake, taking it to Fuuka's room, talking about how you're going to be bonded forever (or in Fuuka's case, wanting the FeMC ALL TO HERSELF), and then you get the fadeout screen with the 'You spent a long time with Fuuka'- the exact same message you get when you max out romantically with a guy. For a game without an explicit lesbian option, they sure do cram in as many non-explicit ones as humanly possible... not that I'm complaining.
 * This troper even had Akihiko comment that FeMC had been up with Fuuka for 'a long time'; the exact same comment he used after she had spent a 'long time' with Shinjiro.
 * He does this after the MAX Rank with Aigis, too. Make of that what you will. If you're lovers with him at the time, it seems almost accusatory.
 * There's even a moment of Lampshade Hanging when Aigis meets the Female Main Character for the first time. Since it features the same hug and declaration as her one with the male MC, Junpei and Akihiko will comment that it's no wonder Aigis wasn't interested in them.
 * Selecting the 3rd option during the last date with Elizabeth leads to some very suggestive dialogue. To top it off you then receive the same "You spent a long time with so and so" message that you get from the male love interests.
 * On that note, in 'Portable' you can choose to have Elizabeth or Theodore as the attendant in the Velvet Room. The route for the dates stays the same, and since you end up inviting Elizabeth into your room and 'spending a long time with her'...

Ho Yay involving other characters

 * Persona 3 suggests such a connection between Fuuka Yamagishi and Natsuki Moriyama, in the way that Natsuki gets really stressed out when she thinks her bullying may have hurt Fuuka a little too much. SEES has to keep Natsuki under constant watch because they think she might have some... issues.
 * Natsuki wasn't afraid here bullying might have hurt Fuuka a little too much. She was afraid her bullying may have KILLED Fuuka. Anyone would react as she did to the thought that a seemingly harmless prank may have accidentally killed someone.
 * It's still played straight after they become friends.
 * Mitsuru also has a particular fangirl that hangs around the main classroom and dreams up elaborate fantasies about her.
 * Said fangirl is also Yandere and Ax Crazy, to the point of blackmailing over people for pictures of and items related to her.
 * And then there's one of the 'bonus' videos added for FES. You know... the one where Yukari drags Fuuka into her bedroom and starts pulling her clothes off so they can pose in maid outfits together? Sadly, the video cuts off there...
 * Akihiko and Shinjiro's relationship in particular seems rather complex, and the Magician Social Link (Kenji) gives the Protagonist a handmade choker when their relationship is maxed out.
 * Aki/Shinji is the most complex relationship, and I swear there's more then enough Ho Yay.
 * More humorously, in the manga's rendition of the Lovers' full moon battle, Akihiko and Junpei end up in a similar situation as Minato and Yukari, and it ends with Akihiko punching Junpei in the face.
 * Not to mention that, in his MAX Rank on the lover's path, before he'll do anything, he asks FeMC to call him "Aki" - as in, the nickname only Shinjiro called him.
 * And poor "Aki" feels quite awkward around girls, and even chatting them up.
 * Jin and Takaya. They hold hands. They go everywhere together. They scheme to They run a  together. And Takaya's last line of the game is "Jin." Ho Yay? For sure.
 * Not to mention Jin's bottomless devotion to Takaya is his main motivation for following the plan to It just makes one wonder what else Takaya could convince Jin to do for him...
 * Jin holds Takaya's hand twice, to stop him from "being reckless". If that's not enough to go on,  and the second time, he's practically begging "Don't Go!" when he looks up at Takaya.
 * This might be a stretch, but Takaya and Jin are always referred to as partners, which doesn't go without a double meaning; Akihiko in particular sounds scathing when he says it, but Jin doesn't care. Hmm...And while they're part of a trio, but they don't seem to care much for Chidori, especially since they
 * Also, this is probably just a coincidence, but Takaya and Jin's names are similar to Tatsuya and Jun, a possibly canon Ho Yay pair in Persona 2: Innocent Sin.
 * Junpei and Ryoji have no shortage of Ho Yay, oddly despite the fact that they're both ladies' men. Only a few weeks after Ryoji first shows up, he and Junpei are practically inseparable, to the point of.
 * Yukari and Mitsuru have a lot of Les Yay.
 * For starters, in the Male MC route during the fight in the Love Hotel, the team gets separated, and when you meet Mitsuru and Akihiko again, Mitsuru will frantically insist that nothing happened. When you play the Female MC route, you meet up with Mitsuru and Yukari, and she'll insist the exact same thing.
 * Mitsuru's resolution.
 * Plus during December, Misturu comes into Yukari's room and they discuss things. They come to the same conclusion pretty quickly and they both sit on Yukari's bed . Lampshaded perfectly in this Let's Play.
 * Yukari crying into Misturu, and what looks like Mitsuru holding her to her chest during The Answer.
 * "Well, that's settled, let's go have a bath!"