Tear Jerker / Rupert

• Rupert is obviously crushed when it looks like Bill has betrayed him in "Rupert and Bill in Gameland." It's not obvious even to the audience in the beginning that Bill's just acting to lure the chess king into a false sense of security. It must hurt Bill a lot as well to have to convince his best friend that he would turn on him just to win a game, but he has to do it. This moment during the battle says it all:
  Bill: (after Rupert gets knocked down) Rupert, are you hurt?!
  Rupert: No, Bill, I'M ANGRY!
• Rupert spends the entirety of "Rupert and the Twilight Fan" beating himself up for letting Tong Lai trick him into helping him put Tiger Lily in an enchanted sleep. He keeps repeating "It's my fault," and his voice as he keeps begging the people he needs help from to fix it just sounds so desperate and heartbroken.
• Rupert facing the decision of saying goodbye to his pet firebird Bernie and being informed that being exposed to water would be harmful for the bird in "Rupert and the Firebird". The episode does have a happy ending of Bernie getting to live in the Bird Kingdom, but if it's your first time seeing the episode, you wouldn't be blamed for assuming it would end with Death by Newbery Medal.
• How does Stubbs the cloud pirate force the Four Winds to do his bidding in "Rupert and the Cloud Pirates"? By never releasing them all at once and threatening to harm the ones he has locked up if the ones he releases don't do what he wants. They're forced to hurt people and serve their enemy to protect their family.
• Despite the show somewhat overlooking it, the way Cyril and Cubby are treated by their grandpa in "Rupert and Growler" is quite a sad and horrific case of abuse. Not only does he verbally abuse them constantly, Rupert is allowed to stay in one of their rooms at the hideout, which is a completely run-down, empty, broken, and downright hazardous room. It's clear that their grandpa doesn't even see them as people but tools for his own use. Arguably the worst part: they blindly obey their grandpa with mostly a gleeful attitude, just listening to their authority figure as they're supposed to do, not realizing that this isn't normal treatment.