Kanji's shadow, one of the most blatant Camp Gay stereotypes in existence, is shown as a representation of his feelings towards men, though it is actually a representation of his desire for acceptance in general. Doesn't stop there being a scene where he is kissed by human Teddie.
Golden really plays up the Ho Yay between Kanji and the protagonist:
If you declined all the invitations from the girls on Valentines Day and hung out with the guys, he will give you a Teddie-shaped chocolate, complete with a blushing sprite.
Some dungeon banters have Kanji also making comments expressing attraction towards the protagonist, like "You're starting to look beautiful..." and "Man, do you work out, Senpai? Can I touch your chiseled abs...?" and instantly back-pedaling.
And there's a certain scene where he declares that he wants to become strong in order to protect you, echoing Chie's similar declaration to you in her own social link, (which she did, in fact, say as an expression of her romantic affections).
When asked who you want to see in a swimsuit the choices are the girls and Kanji.
Chie's and Yukiko at the very least have a Romantic Two-Girl Friendship. The conversation on Saki's appearance on the Midnight Channel ("My soulmate is a girl?"). Who was Yukiko's Prince? Chie! Their respective shadows talk about their dependency on one another, with Shadow Chie representing her control over Yukiko and taking the form of a Dominatrix.
It's also worth noting that Yukiko really wants people drop the "scoring a hot stud" thing that her shadow said, she has no problems with it having referred to Chie as her prince, and in fact she continues to do so herself. Her situation comes off pretty heavily as being If It's You, It's Okay, though whether that's for Chie and Yu is debatable.
Shadow Yukiko declaring Chie to be her prince becomes especially eyebrow-raising in retrospect when one looks at her Midnight Channel debut. "I've got my lacy unmentionables on, stacked from top to bottom!" In the anime, she goes so far as to smack her crotch as a bell goes off in the background.
Depending on choices during the Culture FestivalBreather Episode, the Protagonist can also show an interest in cross-dressing and has the option of willingly taking a seat on the girl's side of the table during the Group Date Cafe so that he can flirt with Yosuke or Kanji.
Yosuke tends to say things to the main character that sound at least awkward, if not outright flirtatious. "I'll invite Daisuke; don't want to look like we're dating." "You look like you're good with your hands—uh, never mind." "If I had to choose, I'd choose you! You're so handsome and reliable! Tee-hee!" That and his semi-homophobic behavior at times seems to be an act of Transparent Closet or Armoured Closet Gay.
You can give him a piggyback ride. It could have been even more gay considering the king's game other options were a hug, or sitting on the MC's lap, or laying their head in his lap, but those didn't match Yosuke's number.
The entire Magician Rank 9 scene. It has the wonderfully ambiguous "I have family and friends... and you," as well as "You're special to me, you know?"
The only other person who says you are special is Rise, and it's no secret she loves the MC. The conversation even ends with "You can feel Yosuke's warm trust."
Everybody calls you Senpai (and Sensei for Teddie). Yosuke calls you "partner".
The Rank 8 scene has, if you choose "You were just upset" in Rank 7, the option to hug him around the waist after the rank goes up. Yosuke, who you might think would freak out, just starts sobbing into your chest.
The Rank 5 scene, where he awkwardly asks whether you keep the goods under your futon and if you've ever invited a girl into your room. If you answer the latter in the negative, Yosuke says "I guess you're more of a man's man than I thought!" and the narrator informs you that "Yosuke looks happy..."
A scene in Golden has the two of them sharing an Umbrella of Togetherness. The trope has explicit romantic connotations, but this is the very same scene where Kanji gets very flustered over the idea of doing the same thing with Naoto, his long-time crush, and says that they "would be just like a couple" if they did so...
Daisuke's complete uninterest in women is rather suspicious... Sure, it's explained later he broke up with some girl but still...
Daisuke: Whatever, girls are a pain in the ass! Right MC?
MC: Right on. (+1 friendship)
Kou's "What are we to you?" speech to Daisuke in his Level 9 Social Link.
Taking the Celibate Hero options, such as stating a lack of interest in the Miss Yasogami beauty pageant and telling Yosuke that you have no romantic interest in either Chie or Yukiko, usually leads one of the party members to make a not-so-subtle crack about the Protagonist's sexuality.
Though in episode 7 of the anime, he's just as freaked out by the... atmosphere of the bathhouse level as Yosuke is.
In their defense, that place was just weird.
Speaking of the anime, in episode 12 it's Yousuke who pulls him out of an Heroic BSOD during the fight against Shadow Mitsuo, in a scene that drips with Ho Yay. Not helped by how they start referring to each other in a First Name Basis.
In Golden, if you win the final Midnight Channel Trivia Quiz, aside from getting the trophy which is what most players would go for, the grand prize is Teddie smooching the protagonist.Again, Muscle Blues plays in the background.
Also, Naoto receives love letters from female classmates even after going public about her cross-dressing. And wins a majority of the female votes during the beauty pageant (though that may be due to her refusal to appear in a bikini like the others).
In Persona 4 Arena, Chie certainly seems to have a lot of chemistry with both robot girls, Aigis and Labrys. She even calls Labrys really cute, expresses a profound desire to befriend and protect her (on par with Teddie who wants to be her knight), and cries when she leaves. And, of course, her Ship Tease with Yukiko is stronger than ever.