The utter infuriation on Clark's face near the end of the 5th issue as he implores Luthor to try and reform. He had been very polite and unassuming for the entirety of the story, but Lex's stubbornness causes his mild-mannered facade to shatter in rage.
When Jonathan Kent suffers a heart attack, Superman rushes to him so fast that his hair catches on fire from the friction, but he's still too late.
The Unknown Superman's comment to Jonathan Kent, "It all works out in the end." Becomes one retroactively.
Superman: Pa? ... I.. .Why can't I hear Pa's heartbeat... Pa! Not my Pa! I can save him! I can save everybody! PAAAAA!
This post on the cover to the issue summarizes the sentiment of it quite well.
This single piece of artwork. All Star Superman Episode 6. I swear on my life I am going to meet Frank Quitely one day and I am going to talk to him about this cover. Because itís Superman looking down at his dadís grave and then that look on his faceÖ Itís not sorrow, or regret. Heís not sad, heís not feeling disappointment. His entire body language is just saying one thing. ďIím not good enough.Ē Superman is nearly a god. He can solve any problem, fight any monster, right any wrong. And he canít save his fucking dad. It flies in the face of everything he is. All of his accomplishments, every trophy in his fortress of solitude, he looks down at that stone in the ground and they all turn to fucking dust.
This simple line from the Prime Superman of DC One Million: "This is an indestructible rose from New Krypton. For him. From all of us. In remembrance of all that we are. And all that we will be."
Superman: I love you, Lois Lane. Until the end of time.
In-Universe with Lex Luthor openly weeping as he understands his place in the universe for the first time in his otherwise miserable life, courtesy of briefly experiencing the world through Superman's eyes.
"It's a cruel joke. The mechanistic clockwork of reality, hinging on a precious, impossible defiance of entropy. On Life. And the clockwork doesn't care. It's like... (growing realization) It's like it's all just us, in here, together. We're all we've got."
Really needs to be viewed for the full impact. The way Lex's voice just cracks on that last line seals it.
The film actually manages to out-Tearjerk the comic in the ending, thanks to Christopher Drake's amazing score.