Anytime Wily laughs. His sprite animation nails it.
Just about anything involving the Navi Customizer program Humor in 3-6. When installed, it allows MegaMan to make jokes to Lan when the L button is pressed.
MegaMan Battle Network
The oven is spitting fire due to a virus, so obviously the solution is to soak the entire thing in water.
The ColorMan scenario really sums up the average intelligence of the adults on MMBN land. So WWW had just hijacked Den City's traffic lights, causing automated cars to crash and explode. One of the WWW then provided a solution for the cars that costs a huge sum of 1,000,000 zenny, nevermind that the problem is with the traffic lights, not the cars themselves. And the generic masses just took the bait mindlessly.
Man: It's only 1,000,000 zenny this time! Cheap!
After Lan fixed the first traffic light, he has to talk some grown-ups out from being scammed:
Woman: Sell it to me! I'll pay you double! Triple!
Lan: Please! Calm down!
Woman: Hey, you're right! I don't even have a driver's license!
A scientist has taken a liking to Haruka:
Scientist: Who's that hot thang in the dress? She's my type!! What??? It's your mother? *gulp*
Wily: As soon as I press this button...Bye bye world! [Wily proceeds to prepare to push the button. This involves raising his arm in the air, finger poised, and twitching]
MegaMan Battle Network 2
Lan and co. went camping in Okuden, only to encounter Chaud at the entrance:
Lan: Chaud!? I thought you weren't coming? If you wanted to come, why didnt you just say so?
Duo's Anger Impact attack. He shoots down a ridiculous-looking angry face as an energy beam.
MegaMan Battle Network 5
Yai's "scared" face in Double Team DS. "HEEEEEELP!"
At the end of 5, Regal undergoes a Heel–Face Turn and gives a talk to the heroes like a calm father figure. What makes this scene amusing is that said speech is accompanied by his evil angry mugshot from his villainous days. This was fixed in the Double Team DS re-release, where he gets a new mugshot that reflects his reformed status more.
MegaMan Battle Network 6
A plumber's Navi loses his tool program, and Lan and MegaMan find it in their house's Toilet Comp, stuck to a Mettaur's head. Lan tells MegaMan to delete the virus, but MegaMan doesn't want to since the program looks harmless and doesn't want to touch it.