The "Sonic In Your Face" special had future Sally sending NICOLE to her past self.
Sally choosing to reject the Source and stay with her family and friends.
Antoine vowing to stay by Bunnie even though an upgrade meant she could never be deroboticized.
Mina sacrificing herself to save Sally when Nack tries to shoot her, taking a bullet to the back. Even though she was hurt over Sonic choosing Sally over her, she realized why he did so, and knew she had to save her for Sonic's sake.
The death of Knuckles' father in the future Mobius. It ends with Knuckles standing over his grave as images of Locke and Aurora watch him, smiling.
Issue #130, when Sonic returns after having seemingly died. He bursts into tears upon seeing his uncle, of all people. This immediately lead to his reunion with Sally, in quite possibly one of the most climactic moments in the comic.
"Star Gazing," which features the first appearance of NICOLE's hologram lynx form. She chose to do so after experiencing life in Sally's shoes, and said that even though she was a sentient being, she had never been able to breathe air or feel water before.
NICOLE: I'm already a sentient being, so I know how to think and reason and even understand basic emotions. But I've never been able to breathe air or feel the wind on my face... or touch water. I realized how lucky you are, Sally. Sometimes I want to live the way you do...
The issue closes with Sally reflecting on how she felt like she was seeing the stars for the first time.
Rosie telling the orphans stories on occasion. In one issue they even hold a play, getting Big the Cat to be Eggman and a reluctant Knuckles to be Sally.
Half Heartwarming, half Tearjerker, but when Antoine's father is on his deathbed and Antoine is apologizing for not being good enough as a soldier, his father just flat out tells Antoine that he's been a braver and better soldier then he ever was, encourages Bunnie and Antoine to stay together and marry at some point. His last words seal this.
Armand: I will tell your mother about your deeds, she will be as proud of you as I am. (Paraphrased)
Issue #221. The people of Mobotropolis are now completely against Nicole, sending her off crying. However, she's quickly comforted by Dimitri and Espio, who assure her that she has the support of others and encourage her to be brave. The three begin hoping that they can all be redeemed.
SU#4 has the cliff-side conversation between Shadow and Hope, that single handedly re-ignites Shadow's spirits and encourages him to repeat the mission that he previously failed. And she ends up hugging him after he succeeds.
A minor moment of Heartwarming. In SU#15, the Destructix, who up to this point were more or less empty slates since being introduced, revealed that despite everything that's happened in the comic, the original Fearsome Foursome (Sgt Simian, Predator Hawk, Flying Frog and Lightning Lynx) are True Companions and that no matter what happens in their lives, they have each other's back and went to all the trouble of getting him back from his clan, who would have eventually ditched him, whilst promising Lightning Lynx that they would never do so.
Sonic Universe #17 has a really touching scene where Antoine asks Bunnie if she sometimes wonders whether they got married too early. They come to the conclusion that if it was before the war, then they'd probably be seen as having rushed things...but as Bunnie puts it, they had to grow up fast, and she couldn't be happier being married to him. Aww.
The five pager for #232 has Bunnie worrying herself ragged over not being half roboticised anymore and trying to decide what to do with herself to Antoine, who just listens and comforts her, showing us why they got married in the first place.
Half heartwarming, half awesome, when Elias goes to Harvey Who for help. This is someone who just lost the throne and support of the people, and just lost his sister (And really the only one in the family who's looked out for him) to Eggman. You'd think he'd run off again right? No. He goes to the only one who can help him fight Naugus secretly to protect the people, even though he knows he might not get said help. Elias' resolve is inspiring, and a good indication on how much he's grown.
Universe 43: Geoffrey, after realizing Naugus for what he is, but unable to to do anything thanks to his past treachery, discovers the Secret Freedom Fighters. Upon seeing Shard, he realizes that either Charles or Rotor, and Harvey Who, have built a team to fight Naugus. The smile he has on his face is possibly the first sign of real hope from him in a long time.
From SU#38: After the events of the issuenote involving Snively trying to get Hope to join him in conquering the world with the Iron Queen after breaking her out of jail, Hope was crying due to guilt over thinking that Snively had a shred of decency and Omega of all people tried comforting her, despite not being good at it.
Issue #171 has Shadow reuniting with Maria one last time.
Maria: Shadow...you have to go and protect everyone now. And you'll always have me...
Shadow: ...If I hold you in my heart...! Goodbye, Maria.
After Mina and Nicole reconcile in Issue #237, a heartwarming moment all its own, Mina dedicates the entirety of her next concert to Nicole and then proceeds to rally the people into demanding her return from exile in #241.
Even though the world was rebooted Ian still devoted 252 to wrapping up as many subplots as he could and having moments in the CtC arc showing what he can of the old continuity. He could totally have just started fresh, but he cared enough about the existing fans to provide some closure and let new fans in on some of what they've missed.
Thanks to Genesis wave, Max is healthy again in 252. After all the crap he went through, it's nice to see him finally catch a break.
Nicole comes from the same alternate timeline that Eggman originally came from. Until the crossover, this meant that every single one of her friends before being sent back in time was dead, and the one responsible still screwing things up in the current timeline, Nicole herself completely unawares. However, in the post-crossover timeline, Eggman's somehow managed to have integrated himself as the new Robotnik Prime. This means that Nicole's home timeline was altered as well, since Robotnik Prime never met his counterpart and Endgame never happened, restoring her world to life and the digital Robotnik that originally became Eggman is back on the dying satellite.
In 253, Sonic learns that the Freedom Fighters are all active again, especially when he learns that Sally's doing undercover work and isn't roboticized.
Sonic and Tails being re-united with Bunnie post-SGW. Tails enthusiastically hugs her and grins from ear to ear because he's so happy she's okay.
Issue 256: Sonic is finally reunited with Sally.
An umbrella one for Ct C: as opposed to his usual cockiness and occasional bouts of self-absorption, with how horrifically bad everything's gone recently, Sonic shifts gears completely and tries to be as supportive and optimistic as possible when it comes to realigning his friends memories. It functions as a nice reminder as well for this series' commitment to continuity and character development in a medium that frequently struggles with those parts.
In Sonic Universe #61, the exchange between Team Dark after they successfully snap Shadow out of Black Death's Mind Control, openly admitting to their status as each others True Companions. Shadow even lampshades it.
Shadow: Careful. We're in danger of becoming all buddy-buddy like Sonic's Freedom Fighters.
In Sonic Super Special Magazine #11's "Sonic Comic Origins: Sally - The Exiled Leader", we finally see the extent of how changed King Acorn is compared to his old self: while King Max would have wanted Sally to settle down and stay out of the fight, King Acorn is much more prouder of Sally's role and admits that he'd still worry about his little girl's safety even when she's with her friends.
In Sonic Universe #72, as Sally and Big investigate something for Dr. Ellidy, Sally asks Big what he thinks of NICOLE. When he replies that he likes her because she's nice, Sally questions if he thinks it's weird that she's not organic. Big's response?
Big: Uh... nope? As long as they're nice, I don't care what anyone is.
The fact that Bunnie and Antoine's marriage (one of the few storylines in recent years to be embraced nearly unanimously) not only survives into the new universe, but the artists take care to draw their wedding bands in basically every panel that shows their left hands.
He may be a genocidal carnivore, but Eclipse the Darkling's genuine love and affection for the Dark Arms is truly sweet. He comes off at times as a parent trying to take care of his kids (when not doing something evil).
In Issue 276, Eggman spends a significant amount of time trying to recover Metal Sonic from the Distant Abyss Zone after Silver closed a portal to it behind him. However, Eggman treats it less like recovering a vital resource and more like rescuing his own son, going into a portal that many not open again, full of deadly creatures, by himself with nothing more than the Big Arm to spearhead the effort and risking his hide to fight off a beast native to the zone. Metal Sonic returns the gesture by using the last 1% of his power reserve to fight off the beast, and Eggman grabs him and makes a beeline for the portal.