Oh, so many! A few that occur to me right away:
"Oh yeah, of course, it's a inter-dimensional multi-form from outer space, they're all terrified of wood!"
"This is not going to be big on dignity."
"Two things always guaranteed to turn up in a museum: The home box of a category four starliner, and sooner or later, him. It's how he keeps score."
"We're being chased by statues in a crashed ship. There isn't a manual for this!"
"What happens if the gravity fails?"
"I thought about that."
"We'll all plunge to our deaths. See? I thought about that."
"I thought I'd popped out of the wrong cake. Again."
"Yours is bigger than mine."
"Let's not go there."
"Stop talking, brain thinking, hush." (I say that to my son all the time, he's Mr. Chatterbox)
"Fish from space have never been so ... buxom!"
"Can't we call for help?"
"Yeah, because space is really quite small and there's bound to be somebody nearby."
"Oh please, have you always been so disgusting?"
"No, that's recent."
"Don't diss the sonic!"
The scene where the Krafayis chases the Doctor down the street, followed by Amy scaring the daylights out of him.
"Is this how time normally passes? Realllllly slowly? In the right order?"
Almost anything from "The Lodger"!
"You've only been here three days, they've been the three weirdest days of my life."
"Look at me, I'm a target!"
"Rory, I'm not trying to be rude, but you died!"
"Yeah, I know, I was there."
The entire "Helloooooo Stonehenge" speech to the fleets in "The Pandorica Opens"
"What in the name of sanity do you have on your head?"
"I'm River Song, check your records again."