In "Good Neighbor Goof," after the show manages to play a trope as inherently comedic as an Ironic Echo Cutfor drama, the audience gets to see Pete bellowing angrily at PJ, who is clearly powerless, stammering timidly in response. Pete doesn't let up even when PJ is clearly very ashamed of himself, at which point the music turns sad, and the content of his bellowing turns into an insulting rant about the Goofs, culminating in Pete forbidding PJ from seeing Max. Max, who was hanging from PJ's windowsill at the time and heard the whole thing, starts to cry. And if the audience hasn't yet, PJ delivers a doozy of a Woobiefying line where he simultaneously explicitly states that the day of fun he's had with Max is the only one he can remember ever having and implies that he's going to accept being completely miserable for the rest of his life, crying and smiling that he'll at least have the memories. This does build into a truly Heartwarming Moment when Max and PJ are finally allowed to become friends.
"From Air to Eternity" has one part that's just heartbreaking. After PJ skydives against his will and messes up, Pete yells at him and insults him for it. PJ confesses that he never really jumped out of a plane before then and won a trophy for a video game, which he thought Pete knew. Then, when he's already really vulnerable, Pete falsely accuses him of being a liar and rejects him outright. Seeing poor PJ trying in vain to get back his father's acceptance is hard enough as it is, especially when he ends up kicking his own trophy and knocking himself down in frustration at the futility, but the next scene makes it even worse because we see him disparaging himself for lying, meaning he internalized the spurious accusation. Dramatic Irony adds another layer of sadness, since the audience knows that Pete is being a complete Hypocrite and PJ doesn't. The worst part is this is exactly how some abuse victims behave in real life. At least PJ ends up passive-aggressively Calling the Old Man Out.