During the meeting between the Golden Age Superman and Batman, Superman tries to convince Batman to join them, explaining to him in a completely non-threatening and friendly way why he should help them, how everyone's life would be better if he did so, as everyone on Earth-1 is darker and more twisted than they are on Earth-2. Bruce's answer? "And what about Dick Grayson?" Superman is completely lost for words, proving that Dick Grayson truly is The Heart of the DC Universe.
Before that, during Batman's mental breakdown, he's at his lowest, blaming himself for losing family, not pawns. And then Kal-L shows up to enlist his help. Yes, his goal is to undo this earth and erase this world's Batman, but in a twisted way, he wants his friend's help, even if the friend is from a different world.
Crosses over with Moment of Awesome, but Bart Allen vs. Superboy Prime. When Jay Garrick falters due to his age and Wally West leaves to say goodbye to his family (itself a Heartwarming moment) Prime berates Bart for being stupid, a child, alone, etc. even as Kid Flash drags him into the Speed Force. Bart starts to falter even as he declares "I'm not stupid." At that point, his grandfather, Barry Allen, who had been dead about 20 real-time years, emerges from the Speed Force, grabs Prime in a choke hold and tells him he isn't alone, either.
When Bruce goes on his self-discovery quest, as he has done before, only it'll be different this time; he's not going to be alone because his two adopted sons Dick and Tim are coming with him.
In a meta-sense, the reasoning behind Nightwing's survival - DC Editorial originally wanted to kill off the character in the events of the story, because his status as The Heart of the DCU would send shockwaves throughout the entire company. Geoff Johns outright refused to write it.
There is Superman from Earth Two coming to the aid of Power Girl and showing her the life she had with him and Lois. After she thought she was all alone, someone who didn't belong, it was truly heartening.
Power Girl: [tearfully] You took me in! You treated me like I was your daughter!
Earth 2 Lois Lane: Oh, honey... as far as we were concerned, you were our daughter.
The final assault against Brother Eye in orbit. Just after the strike team managed to knock out Eye's stabilizing unit to send it hurtling to Earth, the defense systems on the satellite activate to bring Batman, the Eye's original creator, down with it. All the while, the Eye is yelling at his "father", saying that after everything, Batman could never trust anyone ever again. Just then, a green aura appears and Hal Jordan (the one guy who best exemplifies the original reason Bats made Brother Eye) comes to get Batman. As they are leaving, Batman says: "I'll take my chances." To the satellite he created because he lost trust in his peers. That's gotta hurt.
A bit earlier, as they storm Brother Eye, Green Arrow asks why Batman invited him on the mission. The two friends had a massive falling out following Batman's mindwipe. So what does Batman, having recovered from a paranoia-induced mental breakdown, say? "To see if you'd come." Ollie smiles and says "The brave and the bold? You've got me all misty."
Golden Age Superman explaining just why he loves Lois.
"When we were married, everyone asked me the same question. "You're Superman. Why Lois Lane?" I knew she was the girl for me the moment I met her. Lois was brutally honest, curious as a cat, and you'd never get the last word in. She was the most human woman I'd ever met. But on the inside she was more super than I could ever be.