- In "Thoughtscape", Jonny and Doctor Quest are subjected to their worst nightmares in Questworld. For Doctor Quest, it's the idea that Jonny, Jessie, Hadji, and Race all died because he failed. Jonny is subjected to the image of his father cruelly dismissing him for being less interested in the sciences than Jessie, and for being an utter disappointment. Cue the real Doctor Quest showing up before Jonny can go over the Despair Event Horizon.
Dr. Quest: Disappointment? Nothing could be further from the truth!
- The ending of "Manhattan Maneater", where the Quests invite one of the gang members to Africa to release the captured tiger back into the wild. The gang member just stands in awe at the beauty of nature and this powerful predator.
- The episode "Nuclear Netherworld", featuring Jonny's Grandpa Doug. The character was one long tribute to Jonny Quest creator Doug Wildey, who had recently passed away.