When you first see the Wasp nest. "That thing is the size of a city!" Also I know this doesn't count, but I love during the last wave of dragons in mission 58 the lady shouts "you damn lizards, you won't get away with this!" Little reference to Godzilla vs Megaguirus there.
Storm 1 was Master Chief before Master Chief was cool. Storm 1 IS the original Master Chief! YouTube: JLP GAMER
While it's not random dialog pairs, I do like all of Despina's post-attack dialog (I can only imagine the captain has an American flag that follows him around so it can flutter majestically behind him) and the one time when the Earth Eater plates turned up and one EDF guy smugly said "This is JUST like in training."
Also, I like that the "do you like the underground" questions are all flagged as orders, which means they only ever get positive responses.
"My tool is a sword of justice!" "Well here's what happens when you bring a sword to a toolfight!"
I like the Despina's line - 'The Despina has missiles! The enemy wasn't expecting that!''. They weren't? I guess they might not have been expecting that I'd call in an ICBM strike 21 meters from where I'm standing, but still...