“Tell the comander his ride’s here” as the Vorlon war fleet jumps in…
“Oh, Mr. Morden, I have not even started with you yet.” —Londo Mollari
“I think I have a problem.” --Dr. Franklin, admitting he’s addicted to stims
“Well, it must be lunchtime somewhere.” --Sheridan, to his interrogator
“I think I loved…Talia.” —Ivanova to Delenn
“Zooty zoot zoot!”–Sheridan, upon the arrival of Penn and Teller–I mean, Reebo and Zooty
BESTER: That is a lie!
SHERIDAN. True. [pause] What is your point?
MARCUS: I am the very model of a modern major-general
I’ve information vegetable, animal and mineral,
About binomial theorem I’m teeming with lot o’ news
And many cheerful facts about the square of the hypotenuse . . .
DR. FRANKLIN: AAAAAHHHHRRRGGGGHHH!
Brother Theo, to Brother Edward-Passing Through Gethsemane
“If you ask God to forgive your sins, he knows what they are, even if you have forgotten. Leave it in his hands!”
“I see they trained you well back home.”
“Yeah, they always said I was carrying around a lot of repressed anger.”
“And?”
“I’m not repressed anymore.”
– Lennier and Marcus in Babylon 5:“Ceremonies of Light and Dark”
Marcus…from recollection… “Like I have always said, you can accomplish more with a kind word and a 2x4 than a kind word alone…”
Morden: What are you going to do? Blow up the island?
Londo: Actually, now that you mention it…
“Alright, I’ll go find a bucket.” -Marcus, offering to help communicate with the First Ones.
“Nothing changes: Decadence, immorality, chaos.” (from Comes the Inquisitor)
“…I will have to get that painted over…” --Londo Molari
A nice pair of quotes, 5 season apart:
“Would you prefer to be conscious or unconscious during the mating? I would prefer conscious, but I don’t know what your … pleasure threshold is.”
–Ambassador G’Kar to Lyta Alexander, *The Gathering *
“Oh, and you mentioned wondering what my pleasure threshold is. I just recently found out. … I don’t have one. Have a very, very nice day, G’Kar.”
–Lyta to G’Kar, Darkness Ascending
“Physics tells us, that for every action, there must be an equal and opposite reaction. They hate us, we hate them, they hate us back. And so, here we are, victims of mathematics.” —Londo
One of my favorite exchanges was a deleted scene from The War Prayer;
Ivanova and Garibaldi are chatting in the garden. Kosh walks in, looks around, and says “Beautiful. I will miss this place, when it is gone.” and walks away. Ivanova turns to Garibaldi and says “I hate it when he does that.”.
Many of my favourite lines have already been put down here.
But can I submit a favourite scene?
There’s no lines, just a background action that made me nearly piss my pants with laughter the first time I saw it…
G’kar has been warned he’s about to be assassinated. However he needs to keep up his ambassadorial activities, and goes out to see a Minbari ceremony. The whole scene is focussed on Delenn and the other Minbari doing their thing. As part of the ceremony, they hand each spectator a small red seed/fruit. In the background, while everybody else is wrapt in the intricacies of the ceremony G’kar looks at his seed, picks it up and swaps it with the one of the person next to him.
I always loved that part.
There was always something satisfying about hearing Londo (Peter Jurasik) saying “Ah, Mr. Garabaldi.”
I only watched the series through once so I can’t remember too many lines, but I did like the scene where Kosh reveals his true form when rescuing Sheridan. To all the races on Babylon he looks like some sort of angel (or whatever equivalent there was in their race) except for Londo. Rather bitterly, amid the jubilation, he simply says that he saw nothing. I liked the delivery of that line 
TECHNOMAGE: You are a very brave man!
VIR: I’ve been working for Ambassador Mollari for two years. After a while, nothing bothers you.
Reminds me of the scene where the Centauri prophetess predicts both Mollari and Vir will become emperor. “One of you will become emperor after the other one is dead.” And after she leaves they’re sitting around giving each other these . . . looks . . .
“…The Emperor himself said I would only be allowed to leave over his dead body. I said: Well, how strange, Mr. Allen said I would only be allowed back on to Babylon 5 over his dead body. With my very busy schedule I can only accommodate so many requests. I know it’s a burden, but you will simply have to wait your turn.”
*Londo to Zack Allen, Epiphanies *
Damn, Londo really did have the best lines