Smuggler story line is FULL of them.

"Is that a hairstyle or did a whomp rat die on your head?"

"Just wait I needed, officer chatter box is here to save the day."

"You like my armor? I polished for this occasion?" - "Your the shinest bounty hunter I ever met."

Smuggler to Imperial Officer:

"Do you enjoy being Skavak's maid Commander?"

In the Revan storyline, as a Bounty Hunter. Solo instance where you go to the underwater lab.

BH- "Who's in charge here?"

BH- "Before you answer, I'm here to kill whoever is in charge"

I'm sorry but the Bounty Hunters have the best responses/quips ingame. Makes me proud.

On Dromund Kaas:

When the captain is talking about how is soldiers were all acting suspicious and the must be traitors, and so he killed them all.

"Turns out they were just throwing me a surprise party for my promotion."

Andronikos' final line in the Taris class missions before having to return to your ship:

"There's the easy way, the hard way and then there's your way...."

Jedi Counselor Story Quest on Belsavis when you access the 2nd Control Station:

Custodian Droid: "Good day. Welcome the to psychiatric unit. A senior republic officer left orders to restrain a dangerous prisoner, suffering from the delusion she is a Jedi."

Sage (who is a Sith Pure Blood): *laughs out loud*

Andronikos is such a great source for these, apparently. Commenting on Hoth:

"Nothing but snow for kilometers either way, and I already can't feel my toes. Whose idea was it to come here again?"

It was his idea, of course.

Don't remember if this has been shown yet, but male smuggler on Belsavis:

-BURN. ;-)

the funniest lines belong to the male inquisitor and the smuggler.

example: don't know why but almost always when the inquisitor says ''Murder and mayhem await'' it seems out of the blue and i always chuckle.

example 2: ''I want to wear robes of solid gold''

HK-51 (upon using the Assassinate Skill)

Target Locked.... Death Imminent

I'm sure someone has mentioned this, but this line with the Commando made me chuckle:

Lieutenant Hollis: "We're trying to break and Imperial occupation on Balmorra. But the Republic's got no ground, no resources, and right now, no chance."

Character: "Whoever said you had a future in recruiting lied."

I don't know if it's been covered, but I thought it was kind of funny.

There's a scene early on in the Imperial Agent story where you're working for a drug-dealer who wants you to fry a rival's eels. Turns out the eels belong to a fellow imperial, and if you side with him, you go back to confront the drug dealer. I don't remember the quote word for word, but it goes something like:

Imperial: "If I ever see you around here again, I'll gouge out your eyeballs and feed them to you!"

Druggie: "Aw...what? Noooo! That's disgusting!"

You: "That....actually is kind of disgusting...."

That's a planetary sidequest, so BH can do it too.

Also the best part -

You: You said you wouldn't kill him!

Guy: He won't be dead. He'll just be blind and have a bad case of indigestion.

There's a scene after you finish the Dark Temple on DK. You return to a sith lord to tell him that his entire research team was killed. He responds with:

"A shame we lost the whole team. At least it wasn't a total loss. We got what we wanted. "

And the fem sith inquisitor's response to THAT:

"That's just a touch chilly....isn't it? "

There's a scene after you finish the Dark Temple on DK. You return to a sith lord to tell him that his entire research team was killed. He responds with:

 

"A shame we lost the whole team. At least it wasn't a total loss. We got what we wanted. "

 

And the fem sith inquisitor's response to THAT:

 

"That's just a touch chilly....isn't it? "

And then he responds with "Hmm. An acurate assessment."

In the Esseles convo where Kilran first appears and the ship's crew is panicking like crazy, there's the line where you yell "We'll fight you and your Imperial lackeys to the bitter end, Kilran!" and the first navigator then says "Ignore that (wo)man! (S)he doesn't represent us!"

It's absolutely hilarious when everyone's walking on eggshells and you blurt out that line.

"Do you prefer your Jedi dead, or still squirming?"

"Dead, my Lord. I'm a simple man."

And...not said by any character, but overheard in general chat while on Tatooine:

"Hrrrmm....The stupid....clouds everything it does. Easy to troll it is."

Jedi starter missions:

the Manneus exchange. cracks me up everytime

Mako, on arriving from Rishi (may not be entirely accurate on the wording, I heard it last night when I was about to fall asleep):

"Welcome to Rishi: beautiful beaches, sunshine, and about 600 active bounties...pity that the Holonet signal's so weak, though. This place would be perfect!"

During the Republic planetary quest on Hoth:

Player Character: The Empire got your Chiss defector, but the data disk was still on his body.

Major Vinson: It is just as well. I am not sure the men really wanted a Chiss hanging around here.

[Explanatory Screenshot]

At the Coronet Star Port:

Imperial Lieutenant: "I told you, sir. The rocket tram --"

Furstrated Imperial Lieutenant: "Is useless if it can't run on schedule."

Imperial Lieutenant: "Sir --"

Frustrated Imperial Lieutenant: "I've got a platoon of combat starved grunts due in Axial Park days ago. What am I supposed to do with them now?"

Imperial Lieutenant: "Calisthenics?"

Frustrated Imperial Lieutenant: "Don't get smart with me."

jedi starter missions:

 

The manneus exchange. Cracks me up everytime

"shud up foo!"