Since it seems to be catching on…
Londo, speaking to Vir: “you moon-faced assassin of joy…”
Ivanova: the “Death Incarnate” speech
Delenn (paraphrasing): " The only human to destroy a Minbari ship is behind me. You are in front of me. If you value your lives, be somewhere else."
Yours?
“Up yours.” Sheridan to Kosh.
Marc
I was going to post that Delenn line, but you beat me to it. Delenn kicks ass in so many ways!
“I think I loved Talia.”
Understanding is a three edged sword.
Once the avalanche has started, it is too late for the pebbles to vote.
G’kar’s farewell to Sheridan stands out for me:
from foggy memory: “When you are friends with someone you give them a part of yourself, and then you are not ever truly apart. But the part of me that is going will miss terribly the part of you that is staying behind.”
That choked me up the first time I saw it.,
Vir to Morden
“What do I want? I’d like to be there when they cut off your head and stick it up on a pole, as a warning to the next ten generations that some favors come at too high a price. I’d wave at it like this(he wiggles his fingers. Can you arrange that for me Mr. Morden?”
Brother Edward:
“I always wanted to know if I would have the courage to stay in the Garden of Gethsemane. Now I know, Theo, now I know.”
G’kar, to “King Arthur”
…no moral ambiguities, they were the bad guys and we were the good guys. And they made a most satisfying thump when they went down."
Kosh to Sheridan: Jump!
Babylon 5 is the shiznit. And season four will be released on DVD in January. (Why are they making me wait so long? 
)
“How will this end?”
“In fire.”
Emperor Turhan to Ambassador Kosh, The Coming of Shadows
“As I look at you ambassador Mollari, I see a great hand reaching out of the stars. The hand is your hand. And I hear sounds. The sounds of billions of people calling your name.”
“My followers?”
“Your victims.”
Elric and Londo, The Geometry of Shadows
“Then I will tell you a great secret, Captain. Perhaps the greatest of all time. The molecules of your body are the same molecules that make up this station and the nebula outside, that burn inside the stars themselves. We are starstuff, we are the universe made manifest, trying to figure itself out. As we have both learned, sometimes the universe requires a change of perspective.”
Ambassador Delenn, A Distant Star
“Yes, yes, Zathras is used to being beast of burden to other people’s needs. Very sad life. Probably have very sad death, but at least there is symmetry.”
Zathras, War Without End, Part I
“The Babylon project was our last, best hope for peace. It failed. But in the year of the shadow war, it became something greater. Our last best hope… for victory.”
Commander Susan Ivanova
“John Sheridan was a good, kind, and decent man.”
“Delenn, wait! You came all this way just to say that?”
“You came just this far to say less?”
Delenn and Dr. Jim Latimere in Babylon 5:“The Deconstruction of Falling Stars”
“My grandfather once told me, ‘The duration’s going to be a lot longer than the war.’”
Captain John Sheridan
Several of my favorites have been taken, so I’ll add:
“This isn’t some deep space franchise. This station is about something!”
“Good luck, captain. I think you’re about to go where… everyone has gone before”
And of course, “Its like I always say, you get more with a kind word and a two-by-four then with just a kind word. Continue.”
Well, I’ll go look for a bucket, then.
Vir’s potential future wife saying something on the lines of
“The Emperor thinks kindly of you Vir. He said you have a charming and well deserved humility.”
"Now get the hell out of our galaxy!"
Captain Sheridan
"No wonder you are cranky! Crotchety? Nevermind!"
Delenn
"You are the one who was. You are the one who is. You are the one who will be."
Zathras
"If you go to Zahadum you will die."
Kosh
"Life and Death in perfect balance. Good day Molari!"
"I was to be a god, you see…"
The mad Emperor Cartagia
"Goodbye, Lord Reefa."
Molari
Does anyone have Marcus’ speech about the goodness of the general unfairness of the universe?
What do you want?
If you don’t know who this is well there’s no saving you.
There was a scene that never made it into an episode that I think is the best of the series.
Ivanova and Sheridan/Sinclair (I forget which one) are standing in the garden when Kosh comes walking in. He looks around, inhales, and says “Beautiful. I will miss this place…when it is gone.” Then he walks away.
Ivanova turns to her CO and says “I hate it when he does that”.
Sheridan’s apology in the second-season finale was also good.
You cannot run out of time. Time is infinite, you are finite Zathras is finite this…is wrong tool.
–Zathras
Ahem. I apologize, I’m sorry. Heh I’m sorry we had to defend ourselves against an unwarranted attack. I’m sorry that your crew was stupid enough to fire upon a station filled with a 1/4 million civilians including your own people. And I’m sorry I waited as long as I did before I blew them all STRAIGHT TO HELL…as with everything else it’s the thought that counts.
–Capt Sheridan’s ‘apology’ for destroying a centuri ship.
“Do not touch me in that fashion. We may sometimes look like you, but we are not you. Never forget that.”
Lennier, while dangling Marcus off the ground with one hand
Big holographic ancient alien teracotta head thing: Zog!
Ivanova: It appears they understand our language, but aren’t willing to speak it.
Marcus (muttering): Who knew they were French.