There are very many to choose from, but I reckon it's:
HACKER: "You mean to seriously tell me that winking at corruption is government policy?"
SIR HUMPHREY: "No, no Minister! It could never be government policy, that is unthinkable! Only government practice."
Incidentally, for my money, the best from Yes Prime Minister is where Humphrey has been cleared of being a Soviet spy, and Hacker addresses him:
HACKER: "Ah! Goofey... er, Humphrey!"
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Actually, I was giving some more thought to the matter, and I realized that there's one dialogue exchange from YPM that sums up the WHOLE series (including YM - at least in my opinion). It's when Hacker gets the idea to abolish the Education Department.
Hacker: I wonder what Humphrey will say.
Dorothy Wainwright (his political adviser): Whatever he says, I want to be there when you tell him.
Hacker: To witness the clash between the political will and the administrative will?
Dorothy: I think it will be the clash between the political will and the administrative won't.
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HACKER: "Are you saying that you help Ministers make fools of themselves?"
SIR HUMPHREY: "In my experience Ministers don't need help..."
I always found every line of dialogue a joy. But I think you'd have to go some to beat the episode from Yes Prime Minister when they were arranging a state funeral for Hacker's predecessor. As I recall, the French president created a diplomatic incident by trying to bring a puppy as a gift for the Queen in violation of quarantine laws.
BERNARD'We've tried everything ... an oil-painting of the puppy -'
HACKER: Can't you get them to stuff it?
SIR HUMPHREY: There's nothing we'd like more - oh, taxidermy? No chance.
FRENCH AMBASSADOR: The President's wife, our First Lady, has set her heart on it. She is determined.
HACKER; Your Excellency, I must ask the President not to bring that bitch with him. Aghast expression from French Ambassador. HACKER:(panicky) The puppy! I meant the puppy.