Arc 5, chapter 5 has Roll's reaction to Bass giving her a haircut—especially when he says he likes her better that way.
From the same chapter, Tron gets annoyed when she sees a picture of Robert with some girls in a paper. Her reaction and following conversation with her boyfriend is really funny.
Robert calling the Gemini Men two-sided paperweights.
During the Gemini Man fight, his merged personality has Robert on the ropes, and decides that a coin toss will determine if he lives or dies. The result shocks him, and as he's wondering how this could be possible, Robert's narration says "Maybe it's cause the coin landed on heads you dummy." The Mood Whiplash makes it even funnier.
Tiesel heads out in the Gustaff, ready to take on two Doc Robots... and falls straight down, crashing.
Tiesel calls a Bikky enemy (a huge, stomping mech) a bunny. Robert thinks it looks more like a frog covered in red paint.
Tron calls Tiesel and tells him to be careful... because he's not like Robert, who gets things done. Tiesel says "Yeah, I know."
Tiesel recognizes that the Mega Man 2 robots/Doc Robots copying their personalities have the same personalities as the Team Fortress 2 classes because he's played the game before.
Robert requests Bass wait before they fight Break Man so he can ask him (Break Man) a question... his name. Bass is confused.
Bass keeps spilling Wily's real plans, which amuses Robert to no end.
The Yellow Devil Mark II speaks like its Powered Up self, entirely in the word "Bumo."
During a sword fight with Robert, Bass says that since Mega Man always had an ace up his sleeve, now he has an ace in the hole: Two swords. Robert is amused by this.
As Wily wonders why Bass still can't defeat Mega Man, Glyde suggests that it's because he's a super fighting robot.
Robert's narration when he walks in on Wily with Gamma is both awesome and funny.
I still hold my ground, my blaster aimed squarely at his face. Wily just looks at me with a grin. The grin just says "I got this here and there's nothing you can do about it".