In Mega Man 2, when you fight Metalman again in Wily Stage 5, if you use his own weapon, the Metal Blade, against him...he dies in one hit.
Same goes for the Pico Master in Wily 2, whose weakness is the next-to-useless Bubble Lead.
And again with the Fake Wily Alien. It absorbs every attack you have except for, of all weapons, the Bubble Lead.
Bubbleman is supposedly the Butt Monkey of the Robot Masters. His weapons are pathetic, he has several Weaksauce weaknessess, and a crippling design flaw makes him unable to walk.
Auto gives Mega Man his normal helmet, his music plays properly this time.
Another from 7: Shoot a Noise Crush with the right timing as you enter the boss room, and it is possible to defeat both Turbo Man and Spring Man before the battle even starts. Shame it only works in their stages.
The ending of 9:
Then that time! And that time! And that time! And that time! And that time! And that time! And that time! And that time!
The fact that the 7th and 8th ones were "recorded" in 8-bit style (you can tell, because Mega Man is the right colors for their respective Kryptonite Factor weapons) is even more hilarious. Also, the scenes with the rebuilt Robot Masters interspersed through the credits.
10 brings us the Overly-Long Gag involving the Wily Castle map, before the final level.
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*
In Mega Man Legends, you can tell the shopkeeper your name is Hippopotamus. He'll refer to you as that for the entire game.
Anytime Tron Bonne acts like a Tsundere to Mega Man. The first meeting for instance, where Tron has been chased up a street light by the little dog Paprika.
In Mega Man Legends 2, after Tron's robot gets blown up in the ruins, the camera pans to Mega Man going really red in the face, and this exchange takes place:
Tron: *Coughing* Well, there goes another good Gustaff, but it doesn't matter, you're too late, we won! Bon is on his way up to the surface with the key. *coughs* What? Why is your face red? Why is everybody looking at me that way?
One Servbot: Um, Miss Tron, your um clothes have been, um, kind of, um, ripped off....
Other Servbot: Actually, your clothes are, um, gooone.
Tron: What... ah... *Screams* ...y-you dummies! Why didn't you tell me before?!? R-retreat, retreat!
Both Servbots: R-R-Roger!
Also, after you fight Klaymoore the second time...his back goes out. The old timer has to, while stammering in pain, ask his partner Bola to take him out of the ruins.
In "Campus Commandos", Wily is stealing a building with an anti-gravity ray. Then Mega takes control of the ray.
Dr. Wily: Mega Man, that's my building! Give it back!
What's even funnier is when Wily reacts by smashing the Skullker's control panels, causing it to fly everywhere.
The Big Shake:
Dr. Wily: Submit, or I will destroy the city. The Mayor: I can't do that... That's slavery! * Music Stops* Dr. Wily: Sounds good to me.
In "The Incredible Shrinking Mega Man", Mega's forced to use a pay phone to contact Dr. Light. This on its own is funny, but what sells it is Light's reaction.
Dr. Light: A collect call from Mega Man!? ...Yes, I'll accept the charges!
In "Master of Disaster", Wily awakens Lotos the genie, who asks him what he wants him to do.
Wily: *gets the happiest tone in his voice* Well....you can start by destroying those meddling robots.
In Terror of the Seven Seas, Wily thinks he's managed to finally kill Mega Man by strapping him to a torpedo and then watching it explode. When Mega Man returns to Wily's floating fortress/super-ship, however, his reaction quickly goes from surprise to an evil chuckle and an attempt at complete and utter overkill. Apparently he has learned his lesson. His delivery of the line is what sells the moment.
Dr. Wily: Mega Man? Impossible! Proto Man: Looks like nothing you got can stop him, Doc! Dr. Wily: Oooh yesss? How about... eighty laser cannons, fifty missile launchers and - hehehe - two thousand pulse power photon neutralizers? He fires them all at once, but they fail. Prompt the Villainous Breakdown as Mega Man begins cutting his way through a steel door. Dr. Wily: Guts Man! Bomb Man! It's Mega Man! Punch him to pieces! Blow him to bits! Pulverize him!
In Electric Nightmare, Dr. Wily takes control of all electrical appliances in the city, making them murderous and apparently mobile. At one point, Mega Man and Roll gets chased by a hot dog wagon which isn't even electrical!
Roll's over-the-top reaction to a cosmetics robot giving her a bad facial.
When Crash Man boasts about how advanced he is, Mega Man asks him where his hands are. Baffled, Crash Man realizes this and actually concedes to the question's logic.