Magog. Not only does he redeem his mistakes, according to the Novelization he actually becomes the Dean of Students at Paradise Island. It's also sweet Manotaur becomes a teacher at Paradise Island, as the Novelization says that his "kind" was finally accepted by the Greek women.
Bruce patching things up with Dick. All we see is a handshake and it says it all. In the Novelization they tearfully hug, marking the only time many of his colleagues ever saw Bats cry. Including Dick.
At the end, in a Super Hero-themed restaurant, The Spectre discovers there's a (rather plain) meal named after him ("Spinach and cottage cheese? That's a Spectre Platter"), to which Norman replies "Look at it this way. It's flattering to be remembered somehow..." The following panel show the Original Sandman's (who died of old age in the beginning of the story) gear on display.
And heck, most of the ending of Kingdom Come is a CMOH. Superman tying Captain Marvel's cape onto a flagpole at the U.N. building, Wonder Woman regaining her Amazonian title, to say nothing of Wonder Woman giving Superman a new pair of glasses, finishing Superman's cycle away from the alien Kal-El he had become back to the human Clark Kent.
Diana on Phillipus becoming the new Wonder Woman: she can have it.
Alan Scott becomes the metahuman representative in the United Nations.
There's also a touching moment in the epilogue in the Novelization in which Diane recognizes The Spectre (while in Jim Corrigan form), saying, "Jim, is that you?", with Jim responding, "After a fashion." Later, while in church, Norm muses that no one noticed that the guy with red hair with a single Skunk Stripe was non-corporeal.
Superman desperately reaching out to Bruce, offering to unite to form the World's Finest Team, because despite Bruce's conviction they have nothing in common, they do: neither wants to see anyone die.
After Bruce's ruthlessness, cynicism and manipulation has taken a forefront throughout the series, his gentle compassion and kindness to the broken Martian Manhunter, who he has sneaked into his meetings with Luthor to help determine the secrets the other man is keeping, is a refreshing reminder of the other side of Batman.
J'onn: What n-now? I want to stay, I want to... muh-matter, I... oh. You... you don't think I'll h-help... Batman: J'onn, you fought the good fight longer than any of us. You've done all that's ever been asked of you... and today was no exception. You've paid your dues, old friend. Go home and rest. Dream of red sands and silent stars.
Look amongst the tiny figures on the ground during the climactic battle. Who's that protecting the fallen Green Lantern? That's right, it's his daughter Jade, who up to that point was on the other side of the conflict.
It happens also with other daughter/dad pairs: Nightstar saves a wounded Red Robin; Kid Flash saves Flash from Thunder and Jakeem, then carries him closer to Jade's energy shield.
Batman admits despite his estrangement with Dick, he sent gobs of money to every scientist with xenobiology in their background to find a cure for Starfire's illness (she still died), without Dick knowing about it.
When Bats finds out - to his surprise, no less - that Talia is alive and basically Mother Therese's successor, he drops everything to fly to India. Without even a second thought.
Norman's relationship to The Spectre in the Novelization. During the entire novel, Norman is helping him rediscover what it is to be human again - which is a parallel plot to Superman's own rediscovery.
Magog saving as many metahumans as he could, seeing the distant green glow of Lantern's ring in the Novelization, starting with Tokyo Rose.
Magog: Rosie, hold onto your spandex.
Spectre dropping McCay back at his church after Norman singlehandedly averts the Apocalypse.
"Farewell, Norman McCay. You have walked with the titans of the earth... and you have kept stride. You are more like them than you realise. You exist... to bring hope.