Several, but some of the best happen during 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.
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.
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.
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.
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.