After Jonathan's father gave his life to stop Dio from killing him, the police lament that the kindness he showed to those around him was gone forever. Speedwagon, however, disagreed strongly.
Speedwagon: You're wrong! All that was good in that man, he passed along to Jonathan! Every bit of it! You can be sure JoJo's gonna live an upright life using what his father gave him! Rich folks are rubbish...watching them flounce about, I wanna throw the whole lot of them into the Thames...but not the Joestars...they're heroic, and merciful, and just...the whole damn lot are giants among men!"
In their youth, Dio all but destroyed Jonathan's relationship with Erina when he stole her Sacred First Kiss. As adults, however, Jonathan reunites with Erina as she nursed him back to health after his first battle with a newly vampiric Dio, and the two rekindle their relationship, ultimately ending in marriage by the arc's end.
When the life-force of Jonathan's Sunlight Yellow Overdrive restored Bruford's humanity, the once-more Proud Warrior acknowledged Jonathan as "a friend from another time", passing his sword "Luck" onto him, and crumbled peacefully into ash without hate for the world.
In a rather sad and twisted way, the ending to Phantom Blood showed that even Dio is capable of love, even if it's distorted by the childhood abuse he's suffered through.
Wang-Chen!! I will not tolerate you humiliating Jojo!! For being able to reduce me to this state, I respect him more than anyone in this world. Now show him the respect he deserves, and give him a quick, painless, and dignified death. 'Have I made myself clear?!!
The look of shock and then sadness on his face when he realizes that Jonathan has died says that Dio was far more human than he would admit.
Although it was momentary, the Time Skip after their childhood was very sweet to see, that Jonathan grew up strong and smart, getting past his past grief, and in the same time, it seemed that Dio made amends and they become steadfast brothers as they win their final rugby match for their colleges together. Of course, it all goes to hell when Dio reveals in monologue that he's still the same slimebag he was in child, but still, the rugby match was an effective heartwarming scene to lure the audience into a momentary sense of security that the two bitter brothers seemingly making amends and walking to their own bright future.
When JoJo and Wamuu part in friendship after the former kills the latter. They may have been enemies, but such was their admiration for each other's cunning and bravery that there was no hatred, only a warm understanding and respect as JoJo gave the ancient warrior his blood to ease the pain of his passing; and Wamuu only dispersed as dust in the wind when he was certain that JoJo took his antidote, dying without regret having met such a great warrior.
Wamuu: I don't have any regrets... I am sincerely happy to have been able to witness your progress. Maybe I roamed more than ten thousand years just to meet you. Farewell, JoJo.
The fact that, Kars, a villain, cares for his comrades. When Wamuu attacks him for stepping in his shadow, Kars merely acknowledges this as him acting on instinct and apologizes to Wamuu. Later, Joseph himself noted that he could sense the hatred that Kars had for the former because of killing Esidisi. Then when Wamuu dies, he writes off his sense of honor as a flaw that made him weak... and then kills a group of vampires that spoke ill of him.
Stardust Crusaders (including the OVA)
In the last episode of the OVA, following a long and sublime series of apathetic-to-sullenass kickery culminating in beating the blood-spurting hell out of his immortal, nigh-onto-godlike nemesis who had just done away with all his companions, Jotaro's tearful smile at the parting scene is a real sunshine moment. Whoever knew he had it in him?
Episode 3 of the anime treats us with a scene of Joseph Joestar, badass hero from Part 2, doting over his physically unwell daughter Holy, brushing her teeth, washing her face, brushing her hair, trimming her nails, feeding her soup, and cleaning her feet. The cherry on top of this scene is Holy jokingly asking her dad to change her underwear, much to his embarrassment. Joseph Joestar, father of the year!
During The Lovers fight, when Joseph is under the effects of the Lovers, Jotaro flips out more than usual when his Grandfather is under attack, showing that he does care a lot about his Grandfather's well being.
Also during this fight, Jotaro shows complete faith in Kakyoin's ability to deal with the Lovers. The whole time he's simply biding his time for Kakyoin and Polnareff to stop the Stand so he can have his payback.
During the ending when Jotaro, Joseph, and Polnareff are parting ways, they engage in a manly three way hug and with tears streaming down their eyes as they bid farewell, having become very close friend in their 50 day crusade to stop Dio.
After Kakyoin comes back to the party after recovering from his eye injuries, everyone is utterly delighted to see him. He even has to tell them to take it easy on him◊, what with both Joseph grabbing onto his arm and Polnareff smacking him on the back.
While Joseph and company were out trying to save Holly, his wife Suzi is left in the care of Rosas. Suzi wants to visit Holly, but Rosas is afraid of what would happen if she learned of her condition. He tries to tell her himself, but can never work up the courage to do so. Finally, during the last leg of their trip to Holly, Suzi reveals that she knew for a while that something was amiss with Holly. Nonetheless, she has the utmost faith in her husband and grandson, and knows that they'll pull through. It's hard to not be moved by that kind of dedication and faith in one's loved ones.
In a show of cross-generational camaraderie, while battling Terence D'Arby in video games, Jotaro and Joseph were able to outwit him and his mind-reading stand Atum by setting Joseph's Hermit Purple to stealthily play the game for Jotaro so Atum would get false readings. All without the two ever communicating the plan to each other: they played off each other flawlessly and played D'Arby like a fiddle.
Iggy, the bad tempered and unwilling member of the Crusaders... sacrificing himself to save Polnareff from Vanilla Ice, after Polnareff had pleaded with him to save himself and run away. It shows how far Iggy had come in the short amount of time he had been with the group, starting with his first appearance of attacking Polnareff and farting on him.
When the group finally gets to Egypt with the new recruit Iggy, Joseph decides to celebrate with having a group shot of the stand users. This shot also is also the last shot of the second ending to the Stardust Crusaders anime, and just shows how the group has become True Companions.
Becomes even more heartwarming when it's shown that Jotaro keeps this picture on his desk in Vento Aureo.
In the anime, Anne the orphan is finally put on a plane back home, since the Crusaders are painfully reminded that she's going to get someone killed with the caliber of opponents they are facing. She's sad that she didn't get to say bye to Jotaro... until she sees him on the runway and proceeds to enthusiastically wish him good luck as she flies away, to which Jotaro responds with a rare smile.
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.
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?
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.
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.
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!
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.
A violent one, but Giorno really shows that he truly will not let evildoers get their way after Black Sabbath's fight, when he transforms a banana into a gun to murder Polpo for killing a poor old man who happened to be there. All the while putting himself in danger and doing off with a potential ally. While this definitely makes him a grey character, just the fact that the death of passerbys is treated as a minor fact by mafiosos (in the manga and IRL) but Giorno will not let it go unpunished really sets the tone for his beliefs.
Narancia's flashback of Buccellati helping him, showing just why he is so loyal to the man.
A major scene where after finding out the Boss plans to kill Trish, Buccellati decides to betray Passione, and the group is forced to make a major decision; follow Buccellati and be branded traitors, or stay with the organization. Of the group, only Fugo states he has no intentions to follow. Abbachio, Mista, and Giorno all step into the boat, choosing Buccellati over Passione. However, the true moment comes from Narancia, who agonizes over what to do, and begs Buccellati to decide for him. Buccellati orders him to stay, since if he can't come willingly, then he shouldn't bother. In the end, the boat drives off without Narancia, leaving him with Fugo. As he watches them leave, Narancia realizes that he and Trish are the same, having been betrayed by someone they trust, and chooses to defy Buccellati's orders and leap into the water, swimming after the boat while screaming for them to wait as Fugo looks on, stunned.
After Abbachio's death, he's shown to be eating in an unfamiliar place, and he hears a strange scraping noise which turns out to be a police officer searching through some broken glass to find clues. After speaking to the man for a few minutes, Abbachio realizes he knows this man...as his dead friend from when he himself was a cop, who died due to Abbachio taking a bribe. Abbachio stands up and begins walking towards a bus parked across the street, muttering "I have to go...I have to go back to my friends..." Given how cold-hearted he was to the others, especially Giorno, the line has a lot of impact.
Emporio calls Jolyne 'big sister' from the moment he meets her, and in turn she's quite protective of him.
Jolyne's absent father, Jotaro, sends her an amulet in prison. Inside is a picture of her parents, but it also maims her finger, so in disgust she throws it away. Turns out that the amulet also contained the tip of a Stand Arrow, which awakens her Stone Free and helps her survive the many dangers of the prison, and later on when Jotaro visits her in Prison they are attacked and cornered by an assassin. Jotaro stops time and moves to protect Jolyne, only to have both his Stand disc and memory disc taken by Whitesnake. Before he passes out, he hands Jolyne the amulet back, revealing that among everything else, it also contains a communicator to signal a submarine to break her out of jail and take her to shore, where she'll be safe. Jolyne finally realizes all that he's done for her, and demands "How can you?!"
Jolyne wrings her wet coat out on fearsome enemy Foo Fighters, revitalizing them even after it had nearly killed her because she realized that it wasn't protecting Whitesnake's discs out of a loyalty to Whitesnake but rather because it was protecting its own identity and intellect, which had only become real after gaining its powers from the Foo Fighters Stand disc. Foo Fighters is so grateful that it possesses the dead body of a prisoner named Etro and uses its great power to aid Jolyne. It even states that until then it had not lived, and was only mindlessly protecting the discs, but after meeting Jolyne it had truly began to live.
Steel Ball Run
Johnny willingly hands over three corpse parts, the very items that have motivated him to come as far as he did, for Gyro's safety. It truly serves as a testament to how close the two have become, over the course of the race.
Toward the end, after years of animosity between them over the death of Johnny's brother, Johnny's father shows up at the start of the final leg of the race to cheer him on. And with one tearful glance from Johnny, we knew they have finally made peace with each other.
George Joestar: Ladies and Gentlemen! Please, please hear me out for a moment. I am that boy.... Johnny Joestar's father... Only now, after all these years do I realize that I have been unforgivably cruel towards him.... (Barely holding his composure) I know... that no matter how much.... I apologize... there may be no way to undo the harm... I wrought on his heart.... But... (trembling in tears) Johnny.... all alone.... My Little Boy.... came all this way from the West Coast to here.... I'm so proud of him! Thank you for hearing me out!"
The story ends with Johnny being able to walk and taking the corpse of Gyro back to his home in Italy. As he leaves, Johnny embraces the breeze of the Atlantic ocean and recollects all the experiences he and his friend shared during the race.
Why don't we pray that we have a safe voyage, crossing the Atlantic and getting you [Gyro] back home... "home... let's go home..."
One of the early chapters has, as a fun starter image, a picture◊ of Josuke with cutouts pointing to various parts of his outfit and body, each cutout magnifying and showing that part in detail. One of those panels points to the middle of Josuke's chest and and depicts an image of Yasuho with a little heart next to it. Awwwwww. A few chapters later, Yasuho herself gets the same treatment◊, and the panel pointing to her heart has an image of Josuke in it. AWWWWWWWWWWWWWWWWW!
Related to the immediately above, when Yasuho is afflicted by some sort of mental illness (extremely frightening for her) and her own mother refuses to help, leading her to break down crying, her first and most immediate goal is to find Josuke because she knows that he will help her.
Norisuke's reaction to Jobin's return; he hugs his son and greets him energetically.
Josuke arrives to meet Yasuho and Tsurugi following their confrontation with Aishou, following Tsurugi contacting him secretly. Yasuho is overcome with tears of joy to see him again, after a comedic moment where he doesn't recognise her due to the plasters over her face, she leaps into his arms and the pair hug and even cry for each other...and laugh about it. Following this, Yasuho and Josuke share a little moment hanging out hand in hand while singing. D'awwwww.
Kira showing that he grew to care about Josefumi or at least deeply appreciated his support in trying to save Holly; when they're confronted by Damo and Yatsuyu and seemingly about be killed, he apologizes for getting him involved and tries to save him, telling him not to worry about him since he's done for anyways. Josefumi crying and apologizing to Kira for the fact that he was going to end up blabbing and trying to save him with the Rokakaka fruit only further cements the genuine comradeship the two developed, which ends up really subverting one's expectations of Kira from the beginning of the arc and making him a much more sympathetic character than his DIU counterpart.
Nanase rescuing Rohan from the ghosts in Rohan at the Louvre. It comes at the cost of his memories, but still.
A minor one, but in Mutsu-kabe Hill when Rohan goes bankrupt, he stays at Koichi's house. Despite Rohan's near-obsessive behavior over him, they managed to stay friends after all those years.
Some of the exchanges between the characters in All Star Battle take the cake.
If Caesar plays against his grandfather Zeppeli, he starts insulting him and calling him names, since he doesn´t know who he is. However, after winning, he somehow realizes it.
Caesar (if Zeppeli loses): What... is this feeling in my chest... feels like I'm proud or something...? Zeppeli (if Caesar loses): I feel like I practiced with a son or a close friend...
If Narancia plays against Fugo, the latter starts insulting him about how Narancia cannot solve the easiest math problems. Narancia, of course, is pissed off. By the time one of them wins, they seem to have calmed down.
And of course, if DIO plays against Giorno. Obviously, Dio doesn't know he is his son, but he notices that he looks familiar. Giorno, on the other hand, immediately recognizes his father and says he always wanted to battle him.
DIO (if Giorno loses): You... I like you... Giorno (if DIO loses): I will use the power I inherited from you to fulfill my dream.
Also related to Fugo, if he and Buccellati fight and Fugo wins, he says this in a regretful tone:
Fugo: I was so determined to follow you... Why didn't I board the boat...?