(unless otherwise stated, all quotes are from the Manga...and from the Colonel himself.)

"Roy Mustang. Rank: Colonel. And one more thing. I'm the "Flame-Alchemist." Don't forget that."

Ed:"You owe me for this one, Colonel."
Roy:"Hearing you say that makes a chill run down my spine..."

Roy:"It's been awhile since we saw each other...why don't we have a cup of tea?"
Ed:"What's so fun about drinking tea with you?"

"I've told my superiors that he lost his limbs in the civil war in the east. I must ask you to keep quiet about his attempts at human transmutation." (referring to Ed)

"Go home and rest. You'll catch a cold."

"You know that I'm the Flame Alchemist, but you still want to fight me? You're a fool!!"

Roy:"You know, next time, could you consider possibly helping us?"
Hughes:"Forget it! Don't try to drag normal humans like me under the big top with the rest of you freaks!"

"If you still plan on making a fuss, would you prefer to be court-martialed for disobeying orders?"

"He's just bitter that a youngster like me has reached the rank of Colonel. Now he's paranoid that I'm going to take his position one day." (referring to Major General Hakuro)

"This is serious! Unless I see his corpse, I can't even relax enough to go on another date!"

Hughes:"But watch out. You'll make a lot of enemies if you join military command at your age."
Roy:"I'm prepared for anything."
Hughes:"Make sure you have as many people around you as possible that understand and support you."
Roy:(silence)
Hughes:"So hurry up and get a wife!"
Roy:"Will you shut up?!"
Lt Hawkeye:"Colonel please be gentler when hanging up the phone."

Roy:"You said you were going to support me by working under me. How are you going to do that now, when you have a higher rank than me? You fool. Promoted two ranks higher in death. Major General Hughes huh...?"
Hawkeye:"Colonel. Aren't you could, sir, with all this wind? Maybe you should think about heading back?"
Roy:"In a minute. What despicable creatures we Alchemists are Lieutenant. Right now... ...there's a part of me that's trying to figure out the details of transmuting human beings. Now I think I can understand why those two kids wanted to bring their mother back."
Hawkeye:"...Are you alright, sir?"
Roy:"I'm fine. Looks like... ...it's starting to rain."
Hawkeye:"But it's not raining..."
Roy:"Yes it is. This is rain."
Hawkeye:"...Yes sir. Let's get back. It's...getting cold out here..."

Ed:"What is it?"
Hughes:"The guys at headquarters say they're too busy to come, so I came here instead to see you off. Oh yeah I have a message from Roy."
Ed:"From the Colonel?"
Hughes (impersonating Roy):" "I won't allow you to die in my jurisdiction because it'd be a pain to clean up the mess." That's what he said."
Ed:"Fine tell him, "understood. I'd never die before you, Colonel, you @#*$ idiot." "
Hughes:"Ha ha ha! They say that the ruder you are, the luckier you are! In that case, you and Roy are gonna live forever!"

"Out of crisis comes opportunity."

(from the "extras" section of the Manga):

"In volume 2 we will be switching protagonists and the series will be retitled "Flame Alchemist."

"What am I trying to accomplish, you ask...? I want to change the dress code so that all women in the military... ...must wear mini-skirts!!