As ruthless as Owlman is, he has a soft spot for Nightwing as his universe's Nightwing was brutally murdered by the Joker. Owlman goes as far as to free Nightwing and ask for his help in taking down Ultraman.
Catwoman flat-out telling Batman that she cares about him and trying to convince him that what happened to Nightwing wasn't his fault.
Cyborg embracing his father, and forgiving him for the imperfect relationship they had before his accident.
The reclusive and emotionally sheltered Will Magnus first scorns and then accepts The Metal Men as his own family, that he feels the need to protect.
Batman & Nightwing's reunion in Issue 6:
Batman: I am not leaving you, Dick. I am not abandoning you. Nightwing: You aren't, Bruce. And you never have.
Rogues' Rebellion #6 has Pied Piper returning to save his friends and Golden Glider waking up to do the same upon hearing his music. When everything is over, they're thanked by the police for saving the city.
Black Manta refuses to reform, but he does leave Aquaman his trident with the message: I'm glad you're not dead.
Lex Luthor's character arc in general:
To convince Bizarro to overcome his fear of the dark, Lex Luthor tells the clone a story about how he overcame his fear of failure. It takes a second to process, but Bizarro is inspired and says his first words.
Bizarro: Bizarro... try.
Lex is surprised by the sudden revelation that his creation is not so mindless after all.
The cherry on top of the heartwarming sundae is that right after Bizarro names himself "Bizarro", Lex immediately follows suit and does so himself.
In Issue 5, we have this from Lex:
Lex Luthor: That's right, Bizarro. Blockbuster was a bad man. You're a good boy.
Aside from Dick and Bruce hugging in Issue 7, we also have Bizarro hugging Luthor. Though the latter is embarrassed, Catwoman admits it's cute.
Lex Luthor's reaction to Bizarro's death showed he had grown fond of him. When beginning the cloning project over again he doesn't want the perfect clone anymore, but one exactly like him.
Lex has Ultraman kneeling before him begging for a mercy-kill. Instead of obliging him and giving himself the satisfaction of killing a Man of Steel, Luthor decides to let him live.
The most shocking twist of all: Lex Luthor saves Superman's life. The warm smile he gives afterwards makes you realise why superheroes don't kill their enemies: They are people as well with the potential to be humanity's best and brightest.
Luthor had killed the founder of Kord Industries in Issue #1 so he could assimilate it. When his son Ted Kord offers to sell the company to him to pay his expenses, Lex turns down the offer, saying that Kord Industries should remain a family business.
Luthor: But I will be here if you ever need any advice. I'm only a phone call away.
Ted: Everyone's right about you, Mr. Luthor. You're one of the good guys.