Some fans find it funny that the BLUE Chaos Emerald is what lead Eggman and Wily to meet, thought Capcom came up with the idea, long after the idea of Eggman getting the Blue Emerald occurred, so this is a coincidence.
The relationship between Wily and Eggman is bound to create a lot of these, but let's start with part 3, where the two do an "evil brofist." That's what the sound effect says. Evil Brofist.
In Sonic #248, the titular hedgehog, after realizing he's not about to overpower Mega Man anytime soon, finally uses the speed-complementing geometry of Green Hill to his advantage, landing a solid hit on the Blue Bomber. ...And then he decides to gloat. This ends about as well as you would imagine.
Sonic: *Kneeling on Rock's chest* So. You give up yet?
When Rock turns the tables on Sonic in the next issue, it looks like Sonic's finally going to get a shot in by knocking Rock away from Beat in mid-air. Then Rush jets to Rock's rescue. Sonic's reaction?
Sonic (flat glare): The dog flies. Of course the dog flies.
A lot of the "Off Panel" and "Short Circuit" segments qualify:
In Sonic Universe #52's "Off Panel", meeting the Genesis Unit causes Sonic to flash back to the Console Wars.
Sonic: "The Console Wars are never over! This is for the Saturn! Remember the Dreamcast!"
Mega Man: "Aah! Cut it out! I'm multi-platform!"
Ironic considering Sonic is also multi-platform as well.
In Mega Man #27's "Short Circuits", Eggman and Wily roboticize Big the Cat into "Big Man", their "most powerful Roboticized master to date". When told to "do what he does best", Big Man goes to a nearby pond and starts fishing for Chopper Badniks.
In Sonic Universe #52, Sonic laughs at Megaman for nearly running into a Sonic styled fire trap. Sonic then walks face first into a Mega Man style disappearing block. The looks on both Mega Man's and Tails' faces speak volumes.
Mega Man #26. Sonic is faced with the disappearing blocks. He can't get past them. Mega Man fans sympathize. He does get the hang of them in Mega Man #27.
When the Chaotix decide to go after Protoman in STH #249;
Vector: If we only knew where this base was, we could find this Proto-guy faster.
Sonic:(Sarcasm) I dunno, maybe it's the giant, floating skull-egg thing in the sky?
Vector: I woulda figured it out!
And when they find him, they call him this:
Vector: And none of us even knew what a "Pogo Man" was before this.
Dr Wily is utterly convinced that Sonic has the edge over Mega Man during their face off. Why? Because Sonic is covered in spikes, traditionally a one hit kill in Mega Man's own games!
In Sonic Universe #53, one of the doctors' experimental weapons (Chaos Devil) is marked with the warning "DO NOT TOUCH! (NOT EVEN TO PRANK DR. LIGHT!)"
Mega Man #27 features, among several serious fight scenes, Rouge trying to pry the top of Jewel Man's head off.
An early one, before Rouge is deroboticized, is Napalm Man harrasing Shadow while gloating about his invincibility. Then E-123 Omega comes in annihilates Napalm Man in one panel. The exchange is made doubly hilarious thanks to the dialogue.
Napalm Man: Hahahahaha! None can stand against a walking arsenal like me!
Omega: Please. Back of the line, peashooter. *obliteration*
A rather large portion of what happens in the fight with the Robot Masters in Sonic the Hedgehog #250. Such as the two-page spread of Sonic outrunning Quick Man by running perpendicular across his path and fighting other Robot Masters on the way.
In Part 10, as Sonic and Mega Man make their way to the doctors, they both argue if the whole base is one of Eggman or Wily's design since use traps and enemies from previous encounters.
The reveal in part 12 that Wily and Eggman betrayed each other at the exact same time. They only realize this when Knuckles and Proto Man arrive to beat the snot out of them and their personal weapons fail from a dual sabotage.
Mega Man Dropping the Hammer? It hasn't appeared in a game, but it could happen. Mega Man wielding a hammer with little hearts around it that goes "PIKO"? Hilarious!