In one chapter of Season 3, after Bob stole Sam and Fox's Author Powers, he demonstrates his abilities by forcing Sam to wear a tutu. When Bob realizes that he just pushed Sam's Berserk Button, he panics. Since the chapter no longer exists, this isn't the exact quote, but it's pretty close:
Sam: No, you're not! You're just some old guy who was formerly my boss!
In Chapter 91, Bob reminisces about his Start of Darkness. He recalls the time he was trapped in a cave-in on Pluto, then Tim crash-landed on Pluto and rescued him. Then, Bob learns what vehicle Tim crash-landed into Pluto:
Bob: A bicycle?!? YOU CRASHED A BICYCLE IN SPACE?!?
Tim: Yeah... honestly, I'm not sure of how I did that...
Later, from the same chapter, Nuju gets tired of having Matoro constantly following him around and translating everything he says.
This was also one of the rare cases where emoticons were used in a truly funny manner, though it's not possible to replicate this in TV Tropes formatting. When Nuju yelled at Matoro in bird language, he ended his line with the "burnmad" emote, which Matoro repeated when he translated Nuju's speech.
In Chapter 93, Tim and Jack are confronted by Shade, who recently defeated Bob and has taken over as the new Big Bad.
The chapter concludes with the Rock Raiders, Rahkshi, and Toa Nuva trapped in a jail cell aboard the Executioner, and everything they've tried to use to escape has failed. It seems all hope is lost... and then a Running Gag makes a truly epic and hilarious return.