North Pole Down
- Penn being unable to contact his parents on Christmas Eve. He ends up falling asleep in the living room, holding an old family photo of the three of them together. One of the reasons why he hates Christmas and is utterly disappointed when they have to go to the North Pole.
- The reveal of Sashi's family situation in "Flurgle Burgle". Unlike Penn and Boone, Sashi's parents aren't part of the hero industry. They're civilians who think she works at a fast food joint, so she can't tell them about her accomplishments. Even Larry gets choked up.
Number One, Number Two
- The heartbroken look on Larry's face when Rippen tells him he's being let go. Worse, he immediately covers it up with a smile so that Rippen won't feel bad.
- Scaley and his daughter Amber, who ran away because he wouldn't let her be a deputy. They both miss each other terribly but are too stubborn to reconcile.Penn: You have to tell her how you feel, it's not too late.
Scaley: I've got nothing to say to Amber.
(beat, his expression softens)
Scaley: But if you see her, tell her that her Pa says she's always welcome to come home.
- Although it's minor, Penn freaks out over possibly dying due to drinking poison. It's quite possible that his Near-Death Experience in "Totally Into Your Body" made him paranoid about death.
Shirley B. Awesome
- General Awesome urges the trio to leave her behind so she can fly the helicopter to safety, as the helicopter's remote control is strapped to a bomb. Trust an episode inspired by Toy Story to end with a weep-fest.
- Rippen's Near-Villain Victory and The Reveal that he's responsible for Brock and Vonnie getting trapped in the Most Dangerous World Imaginable.
At the End of the Worlds
- When Penn is unexpectedly knocked off the top of a cliff, and unable to fly because Rippen damaged his jet boots, he flashes back to some happy memories with his friends and parents...then closes his eyes with a peaceful smile. A teenage boy just quietly accepted that he was falling to his death regardless of the fact that Penn is saved in the end.
- Rippen elects himself to stay behind in the Most Dangerous World Imaginable as repayment to Penn, who had saved him from falling off a cliff earlier, even after all of the horrible things Rippen did. Rippen notes that the only other person who would do that is Larry, and that even his own family wouldn't have helped him.
- Meta-Example, but with the passing of Adam West, hearing from Captain Super Captain and Professor Evil Professor one last time.