From the first chapter, all of the forest creatures giving Gon a farewell before he leaves for the Hunter Exam.
Kurapika cheering Gon up after a traumatic encounter with Hisoka on Zevil Island.
The lengths Gon goes to trying to rescue Killua from his crazy family. Kurapika and Leorio coming along to help is just icing on the cake.
From the same arc, we get to meet Canary, one of the Zoldyk butlers. The narrative takes its time noting that she sincerely wished to be friends with Killua even at an early age, but could not because the Zoldycks forbade real social interaction with him. So when he finally leaves the butler's quarters and passes her up without saying a word, it's a little hard to watch. But when Gon, who barely knew her but still saw her need to help Killua, cheerily says goodbye to her on his way out, it's the small smile on her face that she makes as Gon passes her by that makes it all worth it.
"Gon....you are light."
Kurapika revealing his powers to Gon, Leorio and Killua. The act of doing so was a great risk. One of the Troupe members, Pakunoda, had the power to read minds. If they were to be captured and Pakunoda were to read their minds, all of Kurapika's weaknesses would be exposed. Gon begs Kurapika to point a Nen arrow at his heart so that it would kill him if he were to reveal his secret. Killua and Leorio follow suit, agreeing that it was a good option. Kurapika, however, refuses their offer. He says that he would not mind it even if they somehow managed to reveal his secret. He had good friends ..
Before this point, Kurapika is extremely depressed because he believes that the Phantom Troupe had been eradicated, eliminating his primary endeavor. Kurapika has not seen Leorio, Gon and Killua for six months, and soon he reunites with the others at a park. Gon and Killua are having an ice-cream eating contest when he gets there, and, on sight, it is obvious that Kurapika is upset. Gon cheerfully tells him that he should be happy. Now that he doesn't have to worry about the Troupe, he can comfortably recover all of the eyes of his murdered Clan. Then, as Kurapika gets over his shock, Killua promptly shoves a pie in his face. Enter Leorio, and Kurapika laughs for what might be the first time in a while.
Melody in general. Her calming presence and Morality Chain status for Kurapika makes the duo's friendship meaningful and sweet.
Chapter 339. That is all.
And then after that, there's Gon saying goodbye to Aunt Mito. Made even more heartwarming in the 1999 anime when he tells her that as far as he's concerned, she isn't just like a mother to him, she is his mother.
In the manga, when Gon is listening to the message Ging left for him and the recording says that if he keeps listening Ging will tell him about his biological mother, and Gon shuts off the tape without a second of hesitation, knowing that the moment he shuts the tape off it will automatically erase itself. When Killua asks him why, Gon tells him that he doesn't care about who his biological mother may be, because in all other respects his real mother is Mito (and unbeknownst to him, Mito is listening in and hears this).
Knuckle subtly trains Gon on his abilities during their fights together in the hopes that he will get better out of genuine friendship.
Morel's incredible display of sympathy and forgiveness for the original hive ants, including a declaration of protection to their entire race spurned by watching Colt desperately clutch the last Chimera Ant to be birthed by the Queen is an excellent demonstration of what it means to be a hunter.
Knuckle even states during this scene that his kind nature comes from his master. Note that he says this with tears in his eyes.
Knuckle going one-on-one with a huge monstrous Chimera Ant, even though the smart thing to do would be to sit back and let his power do its job, because the monster had humiliated Shoot.
Gon and Killua parting ways with Bisky at the end of the Greed Island arc is this and a bit of a Tear Jerker as well. Gon asks her if she wants to come along to meet his father, but she declines, knowing she'll become even more attached to them if she does. They do eventually meet again in the next arc, but it's still a very tender moment, and one that becomes even more touching in the OVA series, where she tells Gon and Killua they're the best and that she loves them. D'awwwww.
From the same arc— Gon decides the first thing he's going to do when he meets his father for the first time? Introduce him to Killua: his best friend.
Gon telling Killua how glad he is that he met him. The kicker? Killua thinks that Gon has it backwards.
In a weird, twisted way, the numerous measures Illumi takes to protect Killua. Despite his upbringing, he goes to very extreme lengths to protect his little brother. It's definitely YMMV, but it's pretty much his only redeeming characteristic.
Meryem goes on a speech on how sociopathic he is and is about to kill Komugi, then he sees her being attacked by a hawk. He kills it and asks why she didn't ask for help, she answers she didn't want to bother anyone. It serves as heartwarming development of character for someone had previously being perceived as a complete psycho.
Their last moments together. Meryem went from someone who wanted to take over the world to someone who just wanted to spend the last few hours of his life playing a board game with someone he had come to care deeply about. When Meryem tells Komugi the poison is contagious, she tells him she won't leave his side and holds his hand when he starts to lose consciousness, thinking she'll be joining him soon.
The epilogue of the Chimera Ant arc is a pretty solid Bittersweet Ending. Make no mistake that thousands of lives were lost during the battle against the Ants, but in the end not only does an oppressive regime finally get taken down, but some of the more sympathetic Ants involved end the arc better off:
Bronorev and Hina's servant decide to go back into NGL of their own free will. He escorts the servant to one of the villages to talk to a certain person. At first, the townsfolk are frightened, but they allow her to visit one person— her human mother, the grief stricken mother of Reina and Kurt from the beginning of the arc. The two have a tearful reunion, and the townsfolk invite both the servant and Bronorev to a dinner to celebrate.
Reina: H-how did you know it was me?
Mother: I'm your mother, Reina. Of course I know it's you!
Welfin joins Hina and Bizeff on their journey to Meteor City in order to find his old friend Gyro. He claims that he's not afraid of anything anymore and plans to live out his life to the fullest.
Colt has been safe the entire time, and is still raising the mysterious baby that the Queen left, who may or may not be a reincarnated Kite. Upon hearing the child speak, Morel rushes to find Gon and Killua and tell them the news.
Killua orders Nanika to either kill his mother by the end of a thirty minute time limit or give him a kiss on the cheek if he leaves the house safely with her in tow. What follows is a very adorable Smooch of Victory because the latter was fulfilled.
In a rare Pet the Dog from his mother; having viewed Killua's Declaration of Protection over a monitor, she decides to remove the restriction movements she placed on Killua and allows him to watch over Alluka freely.
Leorio and Gon reuniting after Gon's life is saved by Nanika. It's the midair hug that really sinks it.
Ging reassuring Gon that he doesn't need to shoulder all of the blame for the events that transpired during the Chimera Ant arc. In addition, he basically tells Gon that Kite wouldn't have taken him along with him if he didn't think he was capable enough. When Gingwants to be a dad, he can be a dad.
Ging's absolutely flustered reaction to seeing Gon for the first time in years was pretty sweet, too.
Before going their separate ways for what may be the first time in the entire series, Gon, Killua (accompanied by his sister Alluka/Nanika) decide to spend one last day together, goofing around and having as much fun as they can.
After everything that went down in the Chimera Ants Arc, it's a relief to see Gon and Killua having fun together again.
The scene where Gon and Ging trade adventure stories in the anime is very reminiscent of the scene where Killua and Silva sat down and talked about Killua's outings. If one didn't know that they had been separated for a good number of years, they'd never be able to tell.