3x11 - Incubator

In this episode we have two Johns, the John on Moya (J) and the John clone in the neural chip which is now in Scorpy's head.

John-clone: Scorpy, I must be in hell...I kicked it on the table? Awww, I am in hell!

John-clone: Do me a favor, kick the habit before it starts, I'm going to get some air, don't wait up for me.
I haven't seen this ep in a long time, but "kick the habit" is a quit smoking slogan.

Scorpius is trying to explain to the John clone that he isn't really John--
John-clone: All right, Scorp, then what am I? Bootleg? A ghost? Holodeck John? A wandering spirit that ain't got no body?
"I'm so sad and lonely...." Bootleg is something clandestine, like a bootleg copy of a U2 concert would be a copy someone made on a recorder snuck in during the concert. Holodeck John is a reference to Star Trek.

D'Argo explains that Jool and Chiana are about to kill each other--
J: If this sector comes up empty, we'll bag it and get some shore leave.

To Pilot--
J: You're the man!

Scorpius: I jumped ship in an evacuation pod.
John-clone: And you lived happily ever after. Is this fairy tale over yet?
"And they lived happily ever after" is the classic ending to a fairy tale.

Linfer: Scorpius is alive
J: It's another grand Scorpy fake-out

D'Argo, Jool, Chiana, and John are arguing about Linfer's offer--
D (to John): This is exactly the kind of attitude that got Zhaan killed.
J: That's low.
I totally agree with John. I wanted to smack D'Argo for that.

Scorpius: [I] created a special task force to develop wormhole technology.
John-clone: Sweet move. Join the army and get them to pay for your pet project.

John-clone: Well, thanks for the slide show, gotta go.