Funny Moments: Some of the translations, most things to do with Princess, and Slasher calling Zero "Big Ice Cream."
Issue #5 was extremely bizarre, but the idea of having Megaman and X racing in a plot that mirrors Wacky Races is damn funny.
In issue #6 was a major moment of funny because of the villain. Jerimum, a parody of historical bandit Lampião, was soooo Crazy Awesome (and downright stereotypical) that one can't help but laugh.
Moment Of Awesome: Of all people, Wily gets one in the penultimate and final issues where he and his armies defeat pretty much everyone. Only an Unstoppable Rage from Rock saves the day.
Narm: Some of the artwork can kill any drama there might have been in a scene.
Never Live It Down: Okay, so there was rampant nakedness. However, that only started with issue 12 of 16. The comic is now mostly known for this.
Nightmare Fuel: Issue 4. The fact that homeless children are being kidnapped, cyborg-ized, and made to work in the off-world colonies and as sexual servants in the “Suspended Cities” is bad enough; it’s here that we learn that Roll was once a human girl, and was among the many, many victims of Project Lazarus. At one point, the guards enter the room, and one stops to talk with Roll. He “promises” to bring her someplace better, where people won’t slap her just for playing with their children. The scene immediately cuts to her decapitated and mangled corpse.
The cover of #12. Hey, remember that (other) scene from 300?.
The splash page in issue #12 featuring the good guys tied up, in pain, and (mostly) naked.
Paranoia Fuel: Apparently, Proto and Wily both spent the last thirty years planting surveillance cameras everywhere.
Possession Sue: Roll. While her upgrade from “supporting character” to “one of the mains” would be fine, they didn’t stop there. She’s the most powerful and important character in the comic, overshadowing even Megaman, and it’s strongly implied that she’s the only robot in existence with a soul (possibly justified by originally being human). Almost everyone of any nominal importance needs or wants her for one purpose or another, and that includes the Greys; after a while, the comic more or less abandons any pretense of its story being about Megaman.