I don’t even know what game this is as I just overheard it once while my boyfriend was playing. But, it always makes me crack up.
In a slightly dimwitted voice:
“We found a witch, may we burn her?”
I think it was one of the Warcrafts. I keep clicking on NPC’s in WoW but so far, no one has said it.
The name slips my mind, but it had a you against the computer capture the base mode where the game would make comments like “Let’s try that again, monkey boy !”.
Colony Wars Red Sun : “Human beings. So stubborn. So weak.”
GTA San Andreas has tons of great dialog, especially from Ryder, your Eazy-E looking homie:
“Sheeeit… I told you he was crazy!” Ryder’s reaction after taking you to your favorite old barber for a haircut.
“Real dependable… unlike some people…” (it’s funnier when you hear it) Ryder again, bitching at CJ.
“You say you’re down for the homies but all you ever do is complain!” Ryder again bitching at CJ. This quote comes in amazingly handy in a variety of situations.
Referring to guns: “And remember, you didn’t get 'em here. And remember, Emmet is the place to go for guns. I always have quality merchandise and I’ve been serving the community for over thirty years!” Courtesy of Emmet, crazy old gun runner you encounter near the beginning.
Vice City had a few good ones too:
“Dicks! You’re all dicks!” Tommy Vercetti, voiced beyond price by Ray Liotta.
“You gettin’ this down, you four-eyed prick?!” Avery to Donald Love.
“I asked that prick Cortez, he said you’re the real deal.” Diaz, recruiting Vercetti into his employ.
Command and Conquer Renegade isn’t remembered for much but it did have some occasionally hilarious dialogue. For example:
“You’re going up against the whole ship by yourself?!”
“Doesn’t seem fair, does it…? Maybe I’ll shoot left-handed.” Random GDI soldier and Havoc, from the ship mission.
“Gettin’ sloppy… lookin’ good though!” Havoc, lamenting having to kick his leather-clad ex-girlfriend out the back of a moving cargo plane.
In one of the Starcraft cutscenes, a Marine is opening a crate containing a nuclear bomb. The camera pans from the front of the opening crate to the top, where we see a digital-readout monstrosity, surrounded by ice and cans of beer. “Thank God for cold fusion!”
All of Blizzard’s RTSs have the units (at least, those with intelligible speech) say funny things when you click on them too much. My favorites are Artanis, a hero in the Starcraft expansion, who eventually says
“What do you think I am, an orc?”
“This is not just Warcraft in space! It’s much more sophisticated!”
“Yes, I know it’s not 3-D”
and a couple of Night Elf units from Warcraft III, the Dryad:
“I am not the dryad you’re looking for”
“I’ll distract the enemy with my Human Call! <Valley Girl voice> Like, I’m so drunk!”
and the Archer:
“Shot through the heart, and I’m to blame”
“Ooh, I’m all a-quiver”.
Finally, in Myth II, in one mission, you’re sneaking into the back entrance to a castle, and overhear two guards talking.
“So, Bob, you’ve saved up a lot”
“Yup.”
“Well, you must be saving up for something”
“I’ve had my eye on a turnip for quite some time now”
“A turnip?”
“Not just any turnip; the world’s biggest turnip”
“So what do you do with the world’s biggest turnip? Turnip soup for everybody?”
“You don’t just eat the world’s biggest turnip!”
“So, uh, you make a wish on it?”
“Now that’s just silly.”
Actually, she says, “I’m so wasted, I’m so WASTED!!”
I like the mission in Vice City that you get from the porno actress, while she’s in the middle of filming a scene for her next movie:
Tommy: So you want me to whack this guy?
Porn Star: Yes, yes, yes!
Tommy (to cameraman): Uh, is she talking to him or me?
Also, from GTA3:
“Oh, Atsuko, you have a back massager!”
“That is not a back massager.”
“Ooh!”
From GTA : Vice City : “Say goodnight, Mr Diaz !” < BLAM ! > < Black screen >
Circle of Thorns victim, City of Heros : “You tried to steal my soul ! I’m telling !”
Mr Bocor, City of Villains :
"Where to begin? Blackmail first, or corruption? Corruption or blackmail? Ah, these are decisions that make this way of life truly satisfying to me. When one is free to pick the evils one truly desires, that is the delight of a wicked life.
“You’ve been quite an asset to my vile works and, what’s the word… depredations? Yes, depredations works for me.”
“There are those who fight consistently for the side of right, and they are heroes. And then there are those like us, who know how to turn the powers of the world to our advantage without care for the cost to others, and we are called villains. Personally, I would rather be the latter any day.”
Doc Buzzsaw, City of Villains : "I sought only to turn a man into a metal-encased juggernaught of destruction powered by the unknown properties of a mysterious living crystal. How could this have all gone wrong? "
click
‘Glor-doog.’
click
‘WHAAAAAAT?!?’
Love that one. Had it as my alert sound for a long time.
Civ III, have a strong enough military and your advisor lets you know that “good, bad, you’re the one with the nukes,” which has the bonus of referencing Army of Darkness 
The Monkey Island series has tons. I can’t remember many of them right now, but here are a few:
“I always knew that there’d me mushrooms in hell”
“You fight like a dairy farmer”
“How appropriate, you fight like a cow!”
I’m going to have to try and remember some more. And I mentioned the MI games before remembering Murray just now. He alone adds lots.
And then there’s Earthbound. I wish I could remember some from that.
I’ve tried to get that one, but never did. Maybe it’s only in the expansions?
There are some good lines from the diplomacy screen, though. For instance, if you’re negotiating a peace treaty with the Aztecs, Montezuma opens the conversation with “Ah, <your name>, I was just on my way to sacrifice some of your warriors. Wanna come watch?”.
Once, I got a request for a military alliance from Bismark: “I want to make this perfectly clear. Germany’s war with Japan is proceeding according to plan. We do not need any help.” <Germany offers: Alliance against the Japanese>
Or, in negotiations of tribute with a much weaker opponent: "Hah! You think we’re afraid of your puny military?
Um, well, as it happens, you’re correct."
And there are several when another civilization is (trying to) demand tribute from you:
“That’s a nice little civilization you have there. It’d be a shame if anything happened to it.”
“Greetings, <your name>! Would you like to take part in our share-the-wealth program?”
“Don’t think of this as tribute. Consider it as a contribution to the cause of world peace.”
The Warcraft II quotes are classic. I still use them around the house.
Footman:
Don’t you have a kingdom to run?
Why are you still touching me?
Orc Grunt:
Oooohooohoo, that tickles!
Two-headed Ogre:
This way! No, that way!
fart He did it! No, he did it!
Now I’m hungry!
Ogre Mage:
We’re not brainless anymore.
fart We did it!
Orc ships:
Who wants to sing?
extremely off-key orcish singing
Goblin Zepplin:
I can see my house!
Wikipedia has a list of Minsc quotes here. I actually never got that far into BG II, the start felt like it was dragging too much. I might have to dig it out and give it another shot, though. NWN 2 is a bit buggy and bland so far, but it has its moments.
Return to Castle Wolfenstein, if you sneak around carefully:
Guard 1: Now, tell me again, how do ve defuse zis thing again?
Guard 2: Cut ze red wire. Or is the ze green? Hold on vhile I get ze manual.
Guard 1: Ach, it doesn’t matter, ze all look grey to me anyvay.
Bomb: BOOM
Really, the entire set of swordfight insults is genius. And Murray is the single greatest Evil Maniac Bent on World Domination ever created.
Murray: You may call me Murray! I am a powerful demonic force! I am the harbinger of your doom! And the forces of darkness will applaud me as I stride through the Gates of Hell, carrying your head on a pike!
Guybrush: …“Stride?”
Murray: All right then, roll! Roll through the Gates of Hell! Must you take the fun out of everything?
…
Guybrush: What do you know about lifting voodoo curses?
Murray: Oh *sure, *I know a lot about lifting curses. That’s why I’m a disembodied talking skull, hanging on a spike, in the middle of a swamp!
Guybrush: You sound bitter.
Murray: I’m sorry, it’s been a rough day.
…
Guybrush, offering Murray his skeletal arm: If I gave you your arm back, what would you do with it?
Murray: I’d terrorize the South Seas! I’d torture the living! I’d demolish the…er… What I meant to say was, I’d use it to pet kittens.
Guybrush: Nope. You blew it.
Murray: Drat.