Report using his one wish from Nij'd to give Ere her real eyes back and her reaction. Considering how dark the "Yay Agenda" arc was up to that point made that moment even more beautiful. The fact that it came after a major Tear Jerker moment made it even better.
Report's triumphant return at the climax of Chrono Troper: Cross.
Dab Gib showing up to aid the cast against Aelf is notable as well, as it can be seen as a testament to his and Report's friendship in the past.
Ainaveltsac: Naharrud accepting the dying Sir Romra's offer of his helmet so the former could read.
A bit later, a perfectly-fine Yug Gib poking his head out of Naharrud after Ainaveltsac collapsed, revealing that the dullahan had saved most of the castles' denizens.
Gabe and Regnis' reunion at the end of the "Worst Case Scenario" arc after he spent two subjective weeks believing she was dead and blaming himself for it:
Gabe: "Regnis!" [hugs her] Regnis: "Gabe? What happened? You look aweful... and you're choking me!" Gabe: "Regnis, I've just realized something..." Regnis: "What? What are you talking about?" Gabe: *beat* "Please marry me!" Regnis: [pauses in suprise, then smiles warmly] "Sure."
Yug and Doog having a conversation, when Dab of all people shows up. Instead of some sort of confrontation, however, all Doog does is grip Dab in a tight hug, which Yug joins in. Dab merely wanted to remind Doog he was still alive, and you can see that, despite everything he did, Doog still loves his older son.
After a major Tearjerker where Ere finds out she'll never walk again, Retrope tells her that if she had any arms, she'd hug Ere. Cue the ship fics!
And after all that happens? The last panel of the Amaterasu Arc is an entire page. It's Amaterasu and Yui, walking hand-in-hand towards the sunset. It's simple, sure, but in its simplicity, it's a Crowning Moment Of Heartwarming to see at least someone get a Happy Ending in this arc.
The best part? The author revealed that the next arc will be called Belated Happy Ending. It's very likely that Report, Ere, and Retrope, all of whom get Downer Endings, will finally get a Happy Ending.
Subverted hard, actually. The Belated Happy Ending arc actually introduced the Ax-Crazy Susano'o, making the situation even worse.
The only person Report can remember? Ere.
After Aries's death, Retrope goes on a Roaring Rampage of Revenge against her killer. It's awesome, it's sad, but it's also heartwarming to see that Retrope really cared about her.