D: John, Aeryn - are you there?
J:  Oh, I'm hearing dead people.  D, how are you alive?
D:  Long story.  Can I give you a ride?
J:  Absolutely.  In what?
D:  Well, that's gonna be a big surprise.  You stay put, we've got a fix on you.  We'll come to you.
J:  Alright.  You heard him folks.  This is the Alamo.
"I'm hearing dead people" is most likely a reference to "I see dead people," probably one of the more famous lines in movie history.  It's from The Sixth Sense, by M. Night Shyamalan. I double checked and the movie came out in the fall of 1999.  Farscape began airing in 1999, so either John saw it just before his test of Farscape One before he was sucked into the UT, or he saw it when he made his way back to Earth in the Kansas/Terra Firma story arc. The Battle of the Alamo was a famous battle during the Texas Revolution.  The Mexican forces eventually stormed the Alamo killing all the Texan soldiers.   

J:  (about needing to use that weird instrument to transfer the baby from Rygel to Aeryn) I'm really sorry about this, baby.
A:  It's alright.  Just get it right the first time.
J:  Nobody gets it right the first time.

J:  Hey, the cavalry's here.
The Cavalry, horse mounted soldiers, always comes in at the last minute to save the day, although, probably back tracking to the Alamo reference, when the Calvalry, though summoned, never made it.  Maybe John thought the whole rescue idea of D'Argo's was a long shot, he should know better than that by now.  :-) 

J:  (to Aeryn as they are getting ready to jump down a grate to a lower level of the Scarran ship) Alright, ladies and children first. 

Einstien: Time
J:  Flies
Einstien: Time
J:  Bandits
Einstien: Time
J:  Wounds all heels
Einstien: Time
J:  Rosemary and...
Einstien: Time
J:  Time ends
I think Einstien might have been testing John by repeating the same words from Unrealized Reality.  The only part that is different is the last "time" by Einstien, to which John replies, "'s up" in Unrealized Reality.  Instead, in this ep, John replies "time ends." 

Harvey:  Give the man a hard hat. (John throws the hat) Oh, you MBA types.
Hard hats are required fashion wear on a construction site, especially a commercial site.  I don't know what an MBA type is since I try to stay away from them.  MBA stands for Master's of Business Administration.  It is an advanced college degree in business management.   

J:  War and peace.  War and peace.  Did you know that Woody Allen's version is better than Tolstoy's?  Because it's funnier and absolute power corrupts absolutely. 
War and Peace is a lengthy novel by Leo Tolstoy.  I've never read it, mainly because I can't get past the first chapter.  Woody Allen is quoted as saying of War and Peace, "I took a course in speed reading learning to read straight down the middle of the page, and was able to read War and Peace in twenty minutes. It's about Russia."  I looked up Woody Allen on Internet Movie Database and did not find a reference to War and Peace, so I don't know if this Crichtonism means any more than it says.  As for "absolute power" the phrase was spoken, almost word for word, first by Lord Acton in 1887, he stated 'Power tends to corrupt, and absolute power corrupts absolutely."  Acton wrote much and repeatedly warned that that political power is the most serious threat to liberty....a la the Scarrans and the Peacekeepers.

A:  This is what you want.  This is what you want.
J:  No, Aeryn, it is not what I want.  It's just that fate keeps blocking all the exits.  And no matter what I do I just keep circling closer to the flame.
A: Then pull back.  This war is not your responsibility.
J:  You and the baby are my responsibility.  How am I supposed to protect you from the Peacekeepers and the Scarrans and the Tregans and the lions and tigers and bears.
In Greek mythology, the Fates are three women who "control," if you will, humans without much thought or care for life or human challenges.   We, human beings, are almost their toys.  As insects circle closer to the flame, they eventually get too close, burning their wings and dying.  Finally, John again references The Wizard of Oz.  As Dorothy is walking through the forest, she is chanting the Munchkins warning, "Lions and tigers and bears....oh my!" 

J:  (to Stark) Your light, it's not your regular brand.
I had two thoughts here.  The first is to light beer.  There are many different kinds and endless television commercials about light beer.  The second is cigarretes.  Most people who smoke, speaking from experience, find a brand of cigs they like and stick with it.  Switching is not done often and in fact when you need to bum one you....oops, I mean I....typically look around until I find someone smoking my brand and then ask to bum one. 

J:  Alright folks, when things to to hell in a handbasket, we meet here.

Braca:  You're the reinforcements?
J:  No we're the band.  Looks like Kiss was the opening act.
D:  Frell, I'm in the wrong band.
As am I D'Argo, as am I.  Can anyone remember the days when Kiss was a opening act?  The opening act for a concert, is typically an up and coming band who is there to get their music heard and warm up the audience for the real show to follow.  Now in this particular reference John could be referring to Kiss's wildness on stage and their joy in destruction, and comparing it to the sorry state of the temple when they walk in it. 

A:  We should disassemble the weaker munitions - make our own shock grenades.
J:  Arts and crafts, she's gonna be a great mom.
LOL....I love this. 

J:  Jothee, pick up the phone.

D:  Well, we've got to stay.  We've got no choice.  Pilot isn't ready.
J:  You heard the man.  Batton down the hatches.  We stay and defend.
To batton down the hatches means to close the doors and windows tightly and get ready for a wicked storm.   

J:  First scarran you see, you tell him who his daddy is.  You tell him, D'Argo!
John first used "Who's your daddy" in Thanks for Sharing. John is pissed off and gets crazy.  The line goes: 
John: (To Tolvin) You been lyin' to your daddy, boy, and you KNOW you shouldn't lie to your daddy. Who's your daddy? Come on, you know who your daddy is...Who's your daddy?!? D'Argo, tell him who his daddy is.
D: (completely deadpan) I'm your daddy.