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Tear Jerker: Superman: Birthright
Early in Superman: Birthright, Clark explains that the reason he is a vegetarian and that he follows Thou Shall Not Kill is that he can see the aura around all living things, and that he never wants to see it disappear. When his friend Kobe is stabbed, Clark makes quick work of the terrorists, then picks Kobe up and urges him to hold on while he takes him to the hospital. We are treated to Clark's POV, where everything is black and grey, except for Kobe, who is surrounded by an absolutely beautiful, rainbow glow. Then the glow fades... and disappears.
The final panels reveal that in their last moments Jor-El and Lara witnessed the unclear image of a man bearing an "S" shield telling them:
Kal-El: Mother...Father...I made it.
There's also the fact that Superman will never know he got through to his parents.
Near the beginning when it becomes increasingly obvious to the Kents that Clark isn't human, John Kent takes a stroll down memory lane, that ends at Clark's spaceship. Then he snaps, and starts whaling on it with sledgehammer furious at the permanent reminder that his son is so different from him. It's just so sad and disturbing to see a loving father like Pa Kent lashing out like that.
On the villainous side of things, Luthor's entire backstory is absolutely miserable, and his defeat at the end surprisingly poignant.
Superman: "I think he just wanted somebody to talk to."