Kirk: Excuse me… Excuse me… I just wanted to ask a question. What does God need with a starship?
Usually pops into my head when I see any of your garden variety Evangelists on TV asking for donations.
My favorite Garak quotes:
“Truth is just an excuse for a lack of imagination.” (I believe it’s from the same episode, “Improbable Cause.”)
and,
“It’s all true.”
“Even the lies?”
“Especially the lies.”
(from “The Wire”)
My favorite Kirk quotes:
“I’m from Iowa. I only work in outer space.” (ST IV)
And, for its bizarreness:
“I don’t like mysteries. They give me a belly-ache, and right now I’ve got a beaut.” (from “The Man Trap.” It sounds like something a detective would say in a bad noir movie or a parody thereof; it breaks me up every time I hear him say it.)
More later; I know other great quotes will occur to me.
“He’s dead, Jim.”
“Sorry, Niether” Perfect line, perfect delivery.
McCoy never said 'dammit" in TOS. The only time there was a swear word was City on the Edge of Forever, where Kirk says “hell.”
TMP: “In other words…they drafted me!”
McCoy, explaining why he’s back aboard the Enterprise.
In the two part Maquis episode, Sisko, frustrated at Star Fleet’s failure to take the threat seriously, cries, “Earth is a paradise! It’s easy to be a saint in Paradise!”
I like that very much. Even TNG was a stylized, cream-cheese series, but DS9 wasn’t afraid to get down and get its hands dirty. People died, and not everything had a happy ending. The more episodes I watch on Spike, the more the series edges up in my estimation.
Kor in “Errand of Mercy” On the war that was halted by the Organians:
“It would have been Glorious”
Kang: “Be gone. We don’t need a reason to hate humans”
Spock: “For a moment I knew what is was to be happy.” (Context makes this one a gem)
Great lines that are so awful they are great:
“Brain and Brain and Brain what is Brain”
“Gonna Crack my knuckles and jump for joy got a clean bill of health from Dr McCoy”
Garak on the moral of “The Boy Who Cried Wolf”: “never tell the same lie twice”
You know this would make a great game Give a quote and see if anyone can give the speaker the series and bonus points for the episode.
“If you can’t take a little bloody nose, maybe you ought to go home and crawl under your bed. It’s not safe out here. It’s wondrous, with treasures to satiate desires both subtle and gross. But it’s not for the timid.” – Q (Q Who)
Spock, from Obsession:
“Do you smell something?”
Originally, Spock smelled the cloud-creature, but in my house we use this quote rather more frequently for a different purpose…
I rather liked “Data, shut up” from Nemesis. It’s a nice departure from the more traditional “Data, that’s enough” he always used before.
From Voyager, Janeway’s remark after the two Q mate–“That’s it?”
Others:
“I’ve absorbed enough delta radiation to make sure my grandchildren glow in the dark.” -Trip
Solok: I refuse to engage in this… human game of taunting.
Ezri: Did I forget to wear my spots today?
Quark: All that intelligence, and he still doesn’t know what a Hew-mon looks like.
This was going to be my choice. Simply by having the Garak character on the best of the series Andrew Robinson got all the great lines.
Here’s some extras that I like:
Elim Garak: Kiss the girl, get the key… they never taught us that in the Obsidian Order.
Elim Garak: That’s why you came to me, isn’t it, Captain? Because you knew I could do those things that you weren’t capable of doing? Well, it worked. And you’ll get what you want: a war between the Romulans and the Dominion. And if your conscience is bothering you, you should soothe it with the knowledge that you may have just saved the entire Alpha Quadrant. And all it cost was the life of one Romulan senator, one criminal, and the self-respect of one Starfleet officer. I don’t know about you, but I’d call that a bargain.
Dr. Julian Bashir: They broke seven of your transverse ribs and fractured your clavicle.
Elim Garak: But I got off several cutting remarks which no doubt did serious damage to their egos.
And a personal favorite:
Garak takes a drink of root beer
Quark: What do you think?
Elim Garak: It’s vile.
Quark: I know. It’s so bubbly and cloying and happy.
Elim Garak: Just like the Federation.
Quark: And you know what’s really frightening? If you drink enough of it, you begin to like it.
Elim Garak: It’s insidious.
Quark: Just like the Federation.
Actually, in the Doomsday episode, the captain of the other ship says, “I swear to God, Jim it came straight from Hell.”
And if you’re going to bring up Kirk’s shouting Khan’s name, you should provide the link.
Kirk: I don’t like to lose.
Khan: Oh, I’ve given you no word to keep, Admiral. The way I see it, you simply have no alternative.
Spock: Sauce for the goose, Mr. Saavik. The odds will be even.
McCoy: You green blooded, inhuman. . .
In that context, Hell is a place, not a colorful metaphor. 
“You’re investigating Quark?” Sisko asks Odo, after Garak’s shop is bombed.
Odo looks up surprised. “I always investigate Quark.”
Hee hee hee.
Ooh! Ooh! I know this one!!!
From The Naked Time:
Sulu: “I’ll protect you, fair maiden!”
Uhuru: “Sorry, neither!”
Chekov : Perhaps you have heard Russian epic of Cinderella? If shoe fits, wear it!
The root beer exchange is the funniest I’ve heard in this thread that I actually hadn’t seen.
From “Amok Time” (isn’t that the one where Spock gets a woody?)
Bones, in telling Kirk, that Spock has to go home or whatever says something about Spock’s testicles exploding or humping Chekov and then says if Spock doesn’t get home “He’ll DIE!”
It is all in the delivery.
Said with the same delivery and same sense of urgency as “It’s his brain, Jim.”
Two from “Star Trek VI: The Undiscovered Country”:
Kirk (after having a not-so-veiled insulting contest with the Klingon delegation during dinner, and as he wearily unfastens his tunic): “I’m going to bed. Please let me know if anyone thinks of another way we could have screwed that up.”
McCoy, as he and Spock are crawling through an access tube to modify a torpedo; they’re listening to the Klingon general ranting and raving: “I’d give real money if he’d shut up.”
Commodore Decker: “Don’t you think I know that!?” (anguished response to a particulalry important line of questioning)
Q: Worf… eat any good books lately?
(I may have the exact wording a little off here, but…)
Q: You’re dead, this is heaven, and I’m God!
Picard: You are not God, Q! I refuse to believe eternity is this badly run.
Q: Blasphemy! You’re lucky I don’t smite you or something…
Nice legs…
For a Human.