Araki-sensei learned how to draw the male form by studying Ancient Greek art. Maybe that's why JoJo's Bizarre Adventure has way more Ho Yay than is normal for a shounen series. Some of the more egregious examples (such as when Joseph and Avdol were magnetized, and when Narancia heard Mista saying "Giorno, not so hard") are often played for comedy's sake, and the Ho Yay is sometimes lampshaded by the characters in the situation.
In general: Most of Dio's men towards Dio. 99.9% of the cast agrees that the man's got some serious chawryyyyyyyyyyyyyyyyyyyyysma.
Speedwagon states that he wants to help Jonathan in any way he can, even if the only way he can support him is by holding his hands.
The fact that Speedwagon dedicated his entire life and legacy to Jonathan and his family to the point that he never married. While the parallels to Mountain Tim in SBR make it possible in far hindsight that Speedwagon may have had feelings for Erina, the few times where he does appear with her he's usually busy focusing on other things. Like Jonathan.
Battle Tendency is positively overflowing with it, what with it being about a bunch of musclebound men who do combat while covered in oil and wearing next to nothing:
Messina saying that Caesar was worse than a girl when it comes to Joseph.
One of the chapters has a cover image (the page image, in fact) featuring Joseph and Caesar pulling uncomfortably close together in what rather looks like an intimate embrace between lovers.
While another has Joseph swinging around on a vine with Caesar holding on a girlfriend sort of way.
The end of the first confrontation with the Pillar Men has Caesar cradling Joseph's unconscious body in his arms all starry-eyed, like a pair of lovers.
There's literally no reason for Caesar to show up during the scene in Venice after their training except as an excuse to bump into Joseph at juuust the right height that they're a facemask away from kissing.
The first part of Joseph's battle with Wamuu involves him grabbing ahold of a long, thick shaft and coating it in oil so that he can penetrate Wamuu with it ( it's a hammer). Does this also remind you of anything?
And then Wamuu makes him feel inferior by whipping out a much bigger shaft. A stone pillar.
Hell, Joseph's most iconic outfit from this series could count, seeing as it's an unnecessarily Stripperificcrop top which combined with his Scarf of Asskicking and tendency for ridiculous poses ends up making him look some sort of Club Kid.
Promotional material for the anime replaces his pants with ripped jeans belonging to his great-granddaughter Jolyne, and it seems no more out of place.
Wham's blanked out expression in the manga after taking a surprise Ripple attack to the arms during the first stage of the chariot race looks a little suggestive when posted out of context. But the anime takes this even further, where he's drenched in sweat and bouncing up and down in a way that's almost obscene. Needless to say, it wasn't long before someone realized this scene wouldn't look out of place with a Brazzers logo on it◊.
Kars and Esidisi raised Wamuu and Santana from infancy in a rather literal case of Has Two Daddies. Given that there were no Pillar Women left in existence, and they probably lived for centuries more before going into hibernation, you can probably put two and two together.
Bast magnetizing Joseph and Avdul together, especially when Avdul tries to slide off only to get caught by the neighborhood kids with his head stuck to Joseph's belt area.
Polnareff and Avdul's questionable poses in certain artbook scans.
DIO spends a lot of time felling himself◊ and looking at a mirror. That's Jonathan's body we are talking about...
Hol Horse: There's no way your sword can beat my gun.
Polnareff: Oh, what's that? You say I can beat your bum? Oh, you're into that stuff!
VANILLAICE. His profile states that his hobbies include "anything that involves Dio" and the guy completely cuts his own head off the second Dio mentions offhand that he should probably find some blood to drink soon.
Vanilla Ice is the only servant Dio trusted enough to turn into a vampire, and both of them wear similar heart shaped acessories and clothes. Coincidence?
Diamond Is Unbreakable:
But of course! How about the scene where Yoshikage Kira walks into the bathroom while Hayato's bathing? Or even any piece of official art involving Kira and his stand Killer Queen for the matter.
There's another piece of official art that has Killer Queen and The World dancing together in a rather provocative manner. And considering that their owners are both male...
Rohan is a straight up Jerkass, but has a huge soft spot for Koichi, whom he considers his inspiration and Only Friend. However, his near-obsessive behavior over him has freaked out Koichi a few times. He was even willing to kill him in order to inmortalize him in his manga!
Hell, even as Rohan dies in the time-loop caused by the effects of Bites the Dust, he is more concerned about Koichi than himself and he dies saying his name.
Not to mention that in Mutsu-kabe Hill, after Rohan goes bankrupt, he lives for a time at Koichi's house. Make of that what you will.
Josuke and Rohan get a lot of Foe Yay, and despite Rohan openly hates him, Josuke has expressed desire to be his friend. Unsurprisingly, they've become the most popular ship in Part 4.
Tsuji Aya is very appreciative of Yukako's looks. Hell, she even feels her breasts (apparently to gauge their symmetry) and giggles when she gets slapped for it!
There's more than one chapter cover where the Bucciarati team are all over each other.
Pretty much everybody is Les Yay towards Jolyne. Doesn't help that Anasui was originally going to be a girl.
While pretty much all of Dio's minions may as well be gay for him, Enrico Pucci may be the one case where the attraction seems mutual and on equal terms, considering the various flashbacks where they lounge around in bed together, shirtless, discussing the nature of the world, mankind, and Heaven. The biggest example is probably the scene where Dio tells Pucci that he should just use Whitesnake to steal The World and use it to conquer the world himself, and forces Pucci's hands onto his head...but Pucci refuses to do it.
Also, Dio gave Pucci his bone - no, not like that! - which...turns into a child...On second thought, maybe it is sort of like that. Said powers granting Pucci a link to the Joestar bloodline is pretty major, given how he obsessed over Jonathan's body back in Phantom Blood. In which case Pucci talking about how the family must be eliminated for him to reach Dio in 'Heaven' almost sounds like Murder the Hypotenuse.
Quite a few post-chapter sketches have Jolyne and Hermes touching and fondlin each other closely.
Steel Ball Run:
Gyro and Johnny. Just look at some of the volume covers! Especially this one and this one◊!
One of the post-chapter doodles features Mountain Tim and Johnny pressing their crotches against each others'. Seriously. Fitting, considering Mountain Tim is basically AU Speedwagon.
Scarlet Valentine's one-sided affection for Lucy Steel, although at least Scarlet is explicitly into women.
While this part is decidedly an aversion of the series penchant for Ho Yay due to its focus on a heterosexual Official Couple and Male Gaze, even then it occasionally indulges in some from time to time. The scene where Joushuu is patted down for money by a bunch of thugs gives off a lot of molestation vibes.