Josuke has just met his father Joseph for the first time, and he's not happy. It doesn't help that Joseph is almost senile and Josuke has a short fuse. But when the two find and need to save an invisible baby from drowning, Josuke has had enough and tells off Joseph, who cuts his own wrist to find where the girl fell in the water. He does this because he states in his own words "I just wanted to look cool in front of my little boy." Josuke, who had been calling Joseph "Mr. Joestar", from then on calls him dad.
A meta moment of heartwarming: Numerous times Josuke has displayed a surprising amount of cunning and cleverness. The same cleverness that Joseph showed back in Battle Tendency and Stardust Crusaders. Looks like he's a bit more like his father than we thought.
A very sweet call-back to Battle Tendency happens in the manga when old Joseph talks about his favorite music, and "Wham" was mentioned... That's right, sixty-one long years after defeating and befriending the Proud-and-Honorable Warrior-Vampire Wamuu, Joseph still fondly remembers and respects him enough to love even bands that share his name.
An often overlooked moment is how much Ryohei cares about his daughter and grandson. While we only see them interact a few times before Ryohei's death, it's clear that the three are all close, making his death all the more heartbreaking.
This is especially heartwarming since Josuke is a bastard child. Illegitimate children are often treated poorly by others, especially in more honor-heavy cultures like Japan.
On both sides of the fourth-wall, Josuke's anger at his outdated-and-ugly-hairstyle being insulted may seem ridiculous at first, but it is revealed that he modelled it out of respect and gratitude for the mysterious young-man who helped his mother get him to the hospital when he was struck by the same fever that almost killed Jotaro's mother in the middle of a torrential snowstorm. To him, insulting this hairstyle is no less than insulting the boy who saved his life.
Yukako Yamagishi is introduced as a girl who's madly in love with Koichi. Her introductory chapters show her bad side, kidnapping Koichi with her Stand so she can turn him "into a man". The following battle ends with her almost killing herself because of cracks in the cliff. Koichi saves her from a certain death by using Echoes Act 2 in order to paste a "boing" sound so she can bounce back to ground, safe and sound. Several chapters later, Yukako is still lovestruck with Koichi, but some advice from Joseph Joestar guides her to the Cinderella beauty room. She gets a face treatment in order to attract Koichi... and it works! But after 30 minutes, the effects of the beautician's Stand wore off, so she comes back and asks for a more... "permanent" treatment, discovering the beautician's Stand in the process. The following scenes have her trying to conquer Koichi's heart, this time in a more reasonable way. Cue Joseph hitting Koichi and sending him flying into Yukako's breasts. The following scene shows them kissing! A chapter later, her face begins to show some... nasty changes, so she hides from Koichi and goes to take revenge against the beautician. Then, Koichi appears in the beauty room, and Yukako is given a test. Should she choose the right pair of eyes, her face will be restored. Should she fail, well... the results wouldn't have been pretty. She decides to let Koichi choose the eyepair for her. After witnessing Koichi's love for Yukako being mutual, the beautician restores Yukako's face, and compliments Yukako on her "good eye for men". In the end, Yukako managed to achieve what she wanted and becameKoichi's girlfriend!
Going one step further: Aya states that, if Yukako chooses the wrong face, she will be rendered hideous by the failed combination. When Koichi is asked to choose, he picks a face, and then summons his Stand. Why? Because if he chooses wrong and Yukako is turned ugly, he wants Aya to blind him by putting out his Stand's eyes, so that her appearance won't keep them apart. How many lovers would make that sacrifice?
For bonus points, there's Yukako's true Love Epiphany from the aforementioned Echoes Act 2 moment where what happened slowly dawns on her and she falls properly in love with Koichi.
Yukako: You mean you had written it there already? When I was trying to rip Echoes apart... You put those letters on that rock beneath the cliff? You mean that while I was trying to kill Koichi, he was already trying to think of how to save me? I-I've lost completely. No, I lost the moment I first saw Koichi. B-But I love him even more now. I don't care if he completely ignores me. I'm just happy thinking about you, Koichi!
The finale of the anime finally gives us the closure the manga did not: Koichi and Yukako (who brought lunch!) meet at the Angelo Stone, a meeting point for lovers, and walk off holding hands. D'awwww.
A relatively minor one: When Josuke and Okuyasu meet Shigechi and figure out how his Stand can be used to get them money, they convince Shigechi to go along and, this is the important part, agree to a 50/25/25 split of the proceeds with Shigechi getting the bigger piece. So many times in this situation the simple-minded but talented person is manipulated by others. Here, while they are doing so to some degree, they're also being generous by giving Shigechi the majority of the reward. Shame Shigechi had to ruin it by getting greedy.
Furthermore, in situations like this, the scammer usually tries to butter up the victim with false praise. However, Josuke and Okuyasu are genuinely impressed with Shigechi's cleverness, openly acknowledging they would not be able to pull off this scheme without his ingenuity.
A moment of heartwarming that also doubles as a Crowning Moment of Awesome. At the beginning of the Sheer Heart Attack arc, Jotaro ends up saving Koichi multiple times from SHA to the point where he nearly gets himself killed for Koichi's sake. When Koichi decides to stand up against Kira, he is promptly punched through the torso and left for dead. It is at this point that Jotaro regains consciousness and compliments Koichi, saying that "psychologically, you were the winner" before proceeding to approach Kira, deliver a Pre Ass Kicking One Liner, and beat the living hell out of him. In the anime, there's an added still of his facial expression, and for once, Jotaro looks absolutely pissed. After that, he turns around to tell Koichi that he's proud of him and that he's really gotten stronger, finishing it off with a smile before passing out.
Even better when you remember Jotaro has watched friends die before, and he most definitely wasn't going to let it happen again.
Okuyasu reconciliating with the spirit of his big brother.
During the Stray Cat arc, the titular character attacks Shinobu and Kira (who has taken her husband's identity) moves to protect her, declaring "I won't let you harm her anymore. I'll make you disappear!" and holding her in his arms. Later on one of Stray Cat's air bubbles strikes a cactus and causes it to explode, showering them both with cactus needles and Kira worries if Shinobu's eyes were injured.
In a harrowing chapter for Rohan, he becomes afflicted with the Stand Cheap Trick. Said Stand forces the person to not show their back to anyone, lest they be killed, then Cheap Trick clings to the person who saw their back's back, and continues the process. Cheap Trick is mean, nihilistic, and pure evil, and attempts to kill Rohan in a variety of ways. He manages to contact Koichi, who blows him off, thinking he's pranking him. A disheartened Rohan attempts to make his way around town, and eventually sees Koichi return for him, realizing there is, in fact, a Stand on his back, and watching his friend risk his life for him. Rohan is nearly moved to tears by this fact.
Rohan: Koichi... you're the best friend a guy could have.
During his battle with the RPS Kid, he snatches Shizuka from Joseph to win the battle. When the RPS Kid kidnaps her and threatens her with bodily harm unless Rohan gives him a rematch, Rohan gets...heated. It's nice to see the self-centered Rohan become protective over her...well, that is until after the battle, when he realizes he's lost her.
Okuyasu's Big Damn Heroes moment during the Crazy Diamond is Unbreakable arc. Kira lines up a contact bomb point-blank with no way for Josuke to avoid it, until it suddenly changes trajectory, teleported by The Hand and a miraculously alive Okuyasu. While he explains the dream he had, Josuke tells him off, before breaking down into tears of joy and scolding him for not getting up sooner.
The moment gets even better when you hear just what Okuyasu's dream was. He was dreaming of walking towards as blinding light where he found his dead brother Keicho. Keicho asked him where he was going and Okuyasu said that he'd follow Keicho since he always knew what to do. Keicho then tells Okuyasu that he should choose on his own where he's going and Okuyasu decides to return to Morioh. It's easy to imagine that Okuyasu really was dead and that his brother saved him. Keicho really did care about his brother.
Another one related to Rohan: after all is said and done, and Yoshikage Kira is defeated once and for all, Reimi is ready to depart. At first, Rohan tries to cover the sadness about Reimi's departure, but then he realizes that Koichi doesn't believe in his facade, and gets sincere about his feelings towards Reimi.
Reimi: What about you, little Rohan? Will you cry because you miss me so much? [beat] Rohan: Yeah right, why would I miss you? You've already been dead for 15 years! I think I already told to quit acting so clingy... Nothing's changed my mind. Now, do as a good little ghost should and go back to the netherworld! [beat] Rohan: Ok, fine! It's really goodbye now, so I'll tell the truth! I'll miss you! I don't want you to leave, either!
A nice little one from the penultimate page describing what happened to Stray Cat, Shizuka, and Jotaro. It implies that Joseph recovers from the worn down state we see him in this part thanks to the positive influence of having Shizuka as a daughter.
The Invisible Baby's mother was never found... In the end Joseph Joestar adopted her. It goes without saying that his wife, Suzi Q. suspected, "Is this another one of your illegitimate children!?" and the family went through another chaotic period. It is unknown whether this was the cause, but Mr. Joestar, who had been growing dull, has recently returned to good health.
In the anime, after Josuke and Koichi manage to outsmart Hazamada and his Stand Surface/Show Off, a battered Koichi offers Josuke a Fist Bump, which he smiles and reciprocates.
The final opening intro of the anime has a shot of Reimi, Arnold, Shigechi, Aya and Keicho looking down on the still-living cast members from the afterlife.
In a Meta way, some fans of the series have really related to Okuyasu due to their own experiences with Abusive Parents, and it's heartwarming/motivating to see him step out of his family's shadow and find True Companions who treat him with respect.
Unlike Josuke who tends to remain calm but determined when his friends are in trouble until his buttons are pressed too hard, Okuyasu and Koichi are both always vocally distressed about the safety of their friends. Examples like Koichi fearing for Okuyasu's life during Red Hot Chili Peppers, and Okuyasu's worry for Koichi when he had been kidnapped by Enigma stand out.
In the Anime adaptation, not once are the skies of Morioh a clear blue; always substituted with eerie psychedelic greens, reds and yellows, lending an ever present oppressive weight that something awful has stained the very soul of this town... That is until Kira Yoshikage is caught red-handed with his identity revealed to Josuke thanks to Hayato's bravery, at which point the miasma literally shatters like glass to reveal a Glittering Blue Sky with white clouds, symbolizing the light of justice and truth finally shining upon Morioh once more.
After Koichi helps Jotaro in preventing Kira from activating Bites The Dust Jotaro goes on to monologue just how much he's grown to respect and value Koichi as an ally. The fact that it's Jotaro of all people saying this shows just how much he's started to soften up.
Jotaro: Koichi, you truly are a reliable guy. I'm thankful I came to this town and met you.
Not to mention that the ending sequence adds just about every character who's still alive interacting and going about their daily lives. Examples include Okuyasu enjoying at Tonio's with his father in an attempt to heal him (it doesn't, but it does cheer him up), Mikitaka spending time with Toyohiro within Superfly, and the aforementioned scene with Koichi and Yukako holding hands and walking off together.
It should be noted: Most of the closing montage did not actually occur in the manga. The only scenes that occurred after Reimi's farewell were the Kawajiri supper and the scene at Morioh Harbor, with some narration in between. So for many fans who felt the manga concluded abruptly, there was some closure here.