So many good ones. Offhand, my favorites are…
Hot Dog: “You frakked half the fleet, and what do you have to show for it?”
Awesome line. So much more than a zinger.
And Starbuck: “Can we NOT tell her the plan?”
“I may be mad, but that doesn’t mean I’m not right”
“Still not to late to flush them all out the airlock” -Colonel Saul Tigh
“It would take too much time” - Admiral Adama
It’s not really a line, but the Centurions and Lee with the hand signals.
It’s not too late to flush them out the airlock.
Starbuck: “Can we NOT tell her the plan?”
there’s more - just have to rewatch some 
Hey I don’t mean to rush you but you are keeping two civilizations waiting.
That was just a great line there with all looking on.
“how many dead chicks are there?”
“i’ll see you on the other side”
“its almost heavenly. reminds me of you”