Martha Kent's first thought when she comes across an abandoned baby in a spaceship is pick him up and start caring for him. Like a mother.
The Late Mr. Kent
Lois confesses to Superman that, despite her teasing, she really did respect and like Clark (who, as the title would indicate, is believed to be dead at this point); Dana Delany's delivery just breaks your heart.
Supes' farewell to Dan Turpin: "Goodbye, old friend. In the end, the world didn't need a superman... just a brave one."
Turpin's tombstone reads as follows: "Daniel Turpin: Earth's Greatest Hero". In a world of superheroes, there is no higher praise.
Among those attending the funeral are Lex Luthor and Lois Lane (who's been giving Turpin so much hard time, as shown in "Tools of the Trade" and "Apocalypse... Now!: Part II").
Toby Raynes staying at her (implicit) lifemate, Maggie Sawyer's side at the hospital, while Maggie was recovering from injuries. And, later on, at Turpin's funeral.
And of course, the dedication to Jack Kirby at the end.
The dedication, which simply reads: "This episode was dedicated to Jack Kirby. Long Live The King".
Tools of the Trade
The episode has Superman publicly give Turpin thanks for saving him, and Turpin saluting as he flies off.
Lois discovers that Bruce Wayne (whom she is dating at the point) is Batman. As she tends to his wounds, she bemoans how she is sitting atop the biggest story in history, the true identity of Batman, yet there's "not a blasted thing" she can do about it. Bruce smiles at her and says "then you really do care about me".
Little Girl Lost
Superman upon discovering the remains of Krypton, laments that there is no sign anything could have survived, that he is indeed the last of his kind... but then he gets a distress signal from a nearby world. It too had suffered from the explosion of its sister planet, Krypton. From what seems like Superman was too late, that everyone on that sister planet perished too, Superman noticed one sleeping chamber not destroyed from the harsh weather and climate that ruined the planet... and it's still active and working. The life form sleeping inside is still alive, and that lifeform he comes to adopt as his cousin, bringing her back to his adoptive world Earth, Supergirl.
What makes this even more sweet is how even though Clark constantly nags at Supergirl in the two-parter she's introduced... the two seem to act as if akin to a Big Brother and Little Sister, because they are the last of their kind - so they found instant kinship with each other. Daaaw!
When Superman and Supergirl are fighting the Female Furies and they get buried by rubble. Superman instantly gets out of the rubble and then starts digging into the rubble as fast as he can with a concerned face while ignoring the Furies, which ends up getting him beaten up and taken to Apokolips. You can tell his big brother instinct got the better of him to the point of overriding his logic and common sense.
Superman hears the cries and distrust of all the people around him in Metropolis (super hearing after all)...Lois tells him not to listen because the people are wrong. He disagrees saying the people are right, then asks out loud, how can he get the people of his adoptive planet to ever trust him again. Lois's response...
Lois: One person at a time...*they kiss*
From the same episode, Jimmy's "man on the street" moment in the aftermath of Superman's brainwashed rampage. Despite having seen everything that his hero did, the teen doesn't berate him, doesn't express fear, seems angry at the way everybody else is reacting. "Superman's saved the world hundreds of times. We owe him another chance!" No better way to prove that he really is Superman's pal.
Supergirl's last scene in the series. The last time we saw her, she was in critical condition as an indirect result of the actions of a brainwashed Superman. Then near the end, as Superman has beaten Darkseid to a pulp in Apokolips and is about to end him, Kara suddenly arrives talks him out of it, not wanting Clark to lose himself to revenge. Despite being badly battered and wounded, she went to Apokolips by herself just to aid him. Then just as Superman looks down feeling guilty, Kara hugs him, showing her forgiveness. Clark returns the embrace, and the two get ready to return home.
The ending of the episode. Superman gave Jimmy a watch that sends out a signal that Superman can hear, any time Jimmy might be in danger, saying that Jimmy will need it - now that the world knows that the two are close friends. What really hits the mark was the whole episode Jimmy kept denying that someone as important as Big Blue could possibly be his friend, and Superman told him to find a way to "clear up this whole mess" that started in the news stretching the truth about Jimmy's friendship with Superman - as if they were BFFs. But Superman pretty much tells Jimmy, "Yeah, you are my friend, and I'll always have your back."
This is especially true if you remember the beginning of the story where Jimmy describes himself as "just a nobody" to Clark Kent. The Man of Tomorrow takes the time to assure his young colleague that that's not true, both as Clark and as his alter-ego. Moments like this make you realize anew why they call this guy "Superman" - and it's not just his powers.
Upon realising he's not Superman, Bizarro stays behind in a lab about to explode, holding it up so Supes and Lois can escape. The last thing he hears before the building goes up is confirmation of what he wanted to be:
Lois: You are a hero.
There is also this exchange:
Lois: You think he survived?
Superman: I hope so, he had a good heart.
Lois: Of course, he came from good stock.
When Flash and Superman race, they still take the time to pay their toll at the booth, even though the attendant can't see anything except a sudden gust of wind.
The end, where Superman tells Bruce how well Tim was able to take care of things in his absence. "For someone who's supposed to be a loner, you sure know how to pick a partner."
Luminus gives a hostage ultimatum to the Man of Steel, informing him that he has Lois and Jimmy and if he wants them, he'll have to come and get them. Dr. Hamilton reminds him that he's almost completely depowered and warns him that Luminus is trying to trap him. Superman's response? "And doing a good job." Vulnerable or not, the Man of Steel will never give up on someone he loves who needs his help.
The Hand of Fate
Superman goes to retired superhero Dr. Fate for help when an Eldritch Abomination captures the Planet building and transforms all the employees. Dr. Fate refuses to help. So what does our hero do? Taking the minor bit of magic help given him by Fate's wife, Inza, he goes back to the building. Even Fate was touched by this.
Superman: What made you change your mind?
Superman: Something I said?
Fate: Something you did. You went back. You didn't stand a chance and you went back. Till then I thought it was only the forces of evil that wouldn't give up. I was wrong.
Bizarro, finding out about Krypton and in his own warped way deciding he will turn Metropolis into Krypton (blowing it up) actually immediately changes his mind and stops the rocket he had fired when Superman points out Lois will be hurt by the blast.
Once the crisis is averted, Superman finds a solution: he sends Bizarro to a small, uninhabited planet for him to protect. When Bizarro complains that there's no one on the planet for him to protect, Superman simply smiles and says "Actually, I thought of that" and brings out a vicious little alien creature that Bizarro had earlier 'adopted' and named Krypto... and as he sits there on the ground of his new home, playing with 'his dog', he says probably the simplest, but most heartwarming line he ever uttered.
Bizarro: Me am happy now.
In Brightest Day
Even though he has defeated Sinestro, Kyle Rayner still thinks he's unworthy of being a Green Lantern member.
Guardian: The ring has chosen you, Kyle Rayner.
Kyle: But, I'm just an artist. I doodle in the margins of notepads, I daydream about color form and monster trucks. I live half my life in a fantasy world.