When the Reaverbot boss follows Mega Man out of the tower at the start of the game. His reaction is priceless.
When you save the Junk Store man early on, he asks for your name, and you can tell him either Mega Man, or Hippopotamus. If you tell him Hippopotamus, he actually calls you that for the rest of the game.
The Japanese version takes it up a notch: You can say that your name is "Kaba" which besides being Hippo in Japanese is also an instance of being called "baka (stupid)".
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.
Tesiel Bonne: What's the matter? If you don't watch it, you're gonna end up with a big hole in your backside! Ha ha ha ha ha! Roll Caskett: I can't shake them...Mega Man...Mega Man, are you all right? You didn't fall off or anything did you?
Mega Man encounters a painter in Uptown who comments that something's missing from the painting she's working on and asks him what he thinks it needs. The player can either reply "Some red" or "Some talent."
Mega Man Legends 2
Mega Man walks in on Roll taking a bath, and she screams at him over a black screen. When the screen fades back in, Mega Man is back outside pumping his fist in victory. He doesn't even seem to be shocked this time unlike in the previous game, as if he actually meant to do it.
During the battle on Nino Island, after shooting down all the Birdbot assault teams:
Copilot Birdbot: All of our assault teams have been shot down! Green Birdbot: Inconceivablllllle!! Red Birdbot: I told you not to underestimate them! How come we have to go to so much trouble over one little blue guy? Blue Birdbot: *hits the Green Birdbot over the head!* Blue guy!? What are you talking about, me!? Blue!? Huh!? Are you talking about me!? Red Birdbot: No, not you! The guy down there!
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.
Hell, Bola's comment just sells it.
Bola: *poofs in, sighs* I thought I was your partner, not your nursemaid.
Teisel Bonne: Listen up everyone! I want you to take everything that isn't nailed down, you hear me?! I don't want there to even be a toothpick left! Servbot 1: Master Tiesel, we've taken all the supplies and loaded them onto the ship! Servbot 2: What should we do with the toilet paper? Teisel Bonne: We may be pirates, but we're not barbarians. We'll let them keep the toilet paper.
After Tron's robot gets blown up in the Saul Kada Ruins, the camera pans to Mega Man going really red in the face, and this exchange takes place:
Tron Bonne: *coughing* Well, there goes another *coughs* 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 Bonne: What... ah... *screams* ...y-you dummies! Why didn't you tell me before?!? R-retreat, retreat! Both Servbots: R-R-Roger!
The Misadventures of Tron Bonne
In any of the bank robbery stages, shoot a Beacon Bomb at a police car. The Servbots quickly chopshop the thing and come running back to you carrying various car parts, gleefully shouting "Yay! Yay!"