In Episode 53 of Rockman.EXE, while having a party at Yaito's house (whose participants are Netto and co., Masa, Miyuki, Saloma, Mariko, and even the ex-World Three executives), Masa tries to cheer up Mariko by giving him a sea bream. Without looking at her, when he receives a response, he turns around and finds that Madoi was the one who accepted it, biting on and holding onto it like a cat.
GutsMan growing like an ape and taking Roll hostage like in a King Kong movie.
During Stream there's an episode where an evil version of Megaman manages to take his place and wreak havoc. How does Lan see through the deception? At the start of the episode, he used a joke chip on Megaman that covered him in bandages, and when Megaman takes them off Lan didn't tell him that he missed one on his butt. When Lan noticed that Evil!Megaman didn't have one, he realized he was dealing with an impostor.
When Lan's friends see Chaud's haircut in the manga, they compare it to a chick coming out of an egg.
Megaman Hub Mode initially serves as an unstoppable Super-Powered Evil Side that puts Lan in critical condition and makes Megaman go berserk. When they first manage to break him out of it, Protoman immediately punches Megaman in the face. Chaud also does this to Lan in the real world.
Chaud in general is much funnier in the manga. In the anime, he was just a cool guy stoic, but in the manga, he's much more likely to loose his cool and give us a few laughs.
After Lan and Megaman first unlock Hub Style, they don't know how to activate it again in order to show his friends, so they come up with a silly-looking imitation. Then, when they fight Protoman, they attempt to activate Hub Style, and accidentally activate the fake. Protoman promptly punches Megaman in the face.