In preparation for blowing up the Earth, the Atraxi surround the planet with a force field, causing the Sun to look rather spiffy. The nearby bystanders then decide that, even though the entire planet's probably in danger, they might as well take out their phones and get it on film, but it's the Doctor's reaction which truly sells it.
The Doctor: Oh, and here they come. The human race. The end comes, as it was always going to, down a video phone!
"I'M THE DOCTOR, I'M WORSE THAN EVERYBODY'S AUNT! ... And that is not how I'm introducing myself."
And "Delete your Internet history." "Get a girlfriend, Jeff!"
Prisoner Zero changes into Eleven but is met with blank incomprehension by the Doctor, and we realize Eleven has spent the whole episode having no idea what he looks like.
The Doctor: Well, that's rubbish. Who's that supposed to be?
After the Doctor phones up the Atraxi to demand that they come back and answer for threatening to torch the Earth in order to flush out Prisoner Zero, Rory sums up the situation perfectly:
Amy admits that she thought the Doctor was just a madman with a box.
The Doctor: Amy Pond, there's something you need to understand because it's important, and one day your life might depend upon it. I am definitely a madman with a box.
Arguably funnier in retrospect that this was the fact that ultimately caused Amy's life to be saved by her realising this, although it wasn't that funny at the time.
"Meanwhile in the TARDIS" 1:
The Doctor's explanation of the TARDIS' chameleon circuit:
The Doctor: It's camouflage. It's disguised as a police telephone box from 1963. Everytime the TARDIS materializes in a new location, within the first nanosecond of landing, it analyzes a twelve dimensional-data map within a thousand-mile radius, and determines which outer shell would blend in best with the environment! [both the Doctor and Amy grin, then his grin drops] ...And then it disguises itself as a police telephone box from 1963...
Amy asks how long the TARDIS has been disguising itself as a police box:
Amy: How long has it been doing that? The Doctor:Oh, not long.
Amy firing off every single question that comes into her head, while continuing to question the Doctor's sanity re: the bow tie.
Amy: You've got a wooden time machine, do you feel stupid? Sorry, back on the tie.
This exchange, which is quite a lovely callback to a similar scene with Rose and the Ninth Doctor.
Amy:[walking out of the TARDIS in a new time period and on a spaceship for the first time] Im in the future. Like hundreds of years in the future. [sudden realization] Ive been dead for centuries! The Doctor: Oh lovely! You're a cheery one.
When Amy tells the Doctor he looks human, he responds with "No, you look Time Lord. We came first."
When explaining their predicament to Amy:
The Doctor: This isn't a floor. It's a— Amy: A what? The Doctor: Well, the next word is kind of a scary word. You might want to take a moment, get yourself in a calm place, go "Ommmm." Amy: "Ommmm?" The Doctor: It's a... tongue.
As the Space Whale gags we have:
The Doctor: Say "wheeeeee!" [Amy screams instead]
As a tidal wave of vomit heads for the Doctor and Amy.
The Dalek's reaction to the Doctor beating the living daylights out of it with a giant spanner. "You do not require tea?"
When, during the standoff later in the episode, the Doctor tricks the Daleks into not exterminating him on sight by, of all things, bluffing that a Jammy Dodger controls a (non-existent) TARDIS self-destruct and, when later called on it, owning up with the excuse that "I was promised tea!" And then eating it while he runs away. One wonders just how many times that has worked or failed before...
The Doctor: Yeah, well, it's a brilliant noise. I love that noise.
Made funnier by the Word of God that River was pulling his leg about that.
Before they leave the TARDIS, River takes her high heels off of the railing underneath the scanner, as she had hung them there.
Amy: Ooh, Doctor, you sonicked her!
Amy: Oh, are you Mr. Grumpy Face today?
The Doctor: You were right. I am definitely Mr. Grumpy Face today.
The Doctor pretends he wasn't listening in when Amy and River are talking about him. He tries to look engrossed in the device he is fiddling with, which River then points out he is holding upside down.
"I thought they were all dead." "So is Virginia Woolf. I'm on her bowling team."
On self-marriage: "Church had a point if you think about it. The divorces must've been messy."
"You bit me!" This one is even better. Matt Smith actually bit Karen Gillan. Several times. The Confidential episode actually has her a little worried and wondering if he's going to do it. Cut to Smith, who is wearing a look of utter glee: "Absolutely I'm going to bite her arm! Yeah, for sure!"
The Doctor: ...it's a quarter of a mile that way and from there we'll stabilize the wreckage, stop the Angels, and cure Amy. River: How? The Doctor: I'll do a thing. River: What kind of thing? The Doctor: I dunno, it's a thing in progress. Respect the thing. Now, let's go!
Also this one:
River: There's a plan? The Doctor: I don't know. I haven't finished talking.
This explains so much about the Doctor.
"Please just shut up, I'm thinking." It's the deadpan delivery that sells it.
The best thing is that the opening credits start as if that was a dramatic alien attack.
Rory's first time in the TARDIS. As the Doctor is rambling on about how Rory's probably wondering how such a big room is inside a phone box, Rory guesses "It's in an alternate dimension?" just as the Doctor says the same thing. Then the Doctor stops, turns to Rory, and acts all mad at Rory because he likes it when people say "It's bigger on the inside."
"It says here I'm your eunuch..."
The Doctor tries flashing his psychic paper, and instead flashes his oh so very out-of-date library card. How out of date is it? Well the paper is kind of yellowed, and the picture is of William Hartnell twelve regenerations ago.
"Tell me the whole plan!" [beat] "One day that will work."
"We shall call for the steward... if you're lucky." The Doctor looks pleased, and then goes "Oh, Crap!" immediately after.
Rory's pathetic speech.
Rory: So basically, both of our parents are dead from getting the plague. I'm a gondola ... driver so money's a bit tight, so having my sister go to your school for special people would be brilliant. Cheers.
A sixteenth century gondolier in Rory's stag night shirt, thanks to Rory's need for a quick disguise. It's about three sizes too small.
Rory's an excellent source of humour in the episode. To wit:
Rory: Yours is bigger than mine. The Doctor: Let's not go there. [...] Rory: Pfft. Um, we are not her "boys". The Doctor: Yeah, we are. Rory: ...yeah, we are. [...] The Doctor: Do you really want to talk about this now? Rory: I have a right to know! I'm getting married in four hundred and thirty years!
The whole "Stop talking. Brain thinking. Hush!" sequence and the Doctor's reaction to figuring out the villain's plans "Eeeeugh." Especially when he gets Rory to cover Guido's mouth.
Half the line and half the delivery, but definitely: "I'm a Time Lord. You're a big fish... think of the children..."
A little one. When the Doctor is up on the bell tower, he tells the bell to shut up. The face he makes as he does this. He's such a little kid.
His attempts at faking martial arts with a broom (listen carefully he's making lightsaber noises), immediately preceded by "The only thing uglier than you is your mum." Made even funnier by the fact that it gives perfectly the needed effect.
A summary of the whole franchise in two sentences.
The Doctor: There's something here that doesn't make sense. Let's go and poke it with a stick.
Both the Doctor and Amy get one. After screaming how DULL the village they're trapped in is, alternate-reality Amy goes into labor. After both the Doctor and Rory shout "You're a doctor, help her!" at each other, the Doctor simply places his hands between her knees to "catch" the baby. A second later, Amy declares she's faking it and says, "This is my life now, and it just turned you white as a sheet, so don't you call it dull again, ever, OK?"
The swingset scene:
The Doctor: Now, we all know there's an elephant in the room... Amy: I have to be this size, I'm having A BABY. The Doctor: No, no. The hormones seem real, but no. Has nobody even mentioned Rory's... ponytail? [Amy smirks and Rory glares] You hold him down, I'll cut it off! Rory: This from a man in a bowtie? The Doctor:Bowties are cool!
Rory and the Doctor are at it again...
The Doctor: I can't feel my feet... and other parts. Rory: I think all my parts are fine. The Doctor: Stop competing!
Peruvian folk band.
Amy: Oh, my boys, my poncho boys, if we're going to die, let's die looking like a Peruvian folk band.
Rory calling pregnant Amy "Chubbs" earns him a Death Glare.
Amy and Rory hiding in their house:
Amy: I think the baby's starting! Rory: Honestly? Amy: Would I make it up at a time like this? Rory: Well, you do have a history of Amy:[death glare] Rory: being very lovely.
"I carried you [upstairs]. I'm afraid you may experience some bruising."
After Rory cuts off his ponytail, Amy responds "I was starting to like it."
Craig: Listen, Mark and I had an arrangement where if you ever need me out of your hair, just give me a shout. [winks] The Doctor:[winks back] ...Why would I want that? Craig: Uh, in case you want to bring someone round? A girlfriend... [eying the Doctor's clothes]or boyfriend? The Doctor:[realizing] Oh I will! I'll shout if that happens... yes. Something like... "I WAS NOT EXPECTING THIS!!"
There's also this:
The Doctor: Girlfriend? Craig: Friend who's a girl. There's... nothing going on. The Doctor: Perfectly normal; works for me.
The reappearance of "Bowties are cool". One of Amy's normal guy tips is "Bowtie. Get rid!" The Doctor refuses outright, and at this same time, Craig is talking with Sophie and tells her one of the Doctor's oddities is he wears a bowtie.
The shower scene! The Doctor literally falls out of the shower, barely gets a towel around himself, and then rushes out to save the day... and only then realizes that he isn't holding the screwdriver.
Craig: Well, if I ever am [in trouble], you can come save me... with my toothbrush.
Here's another bit that's barely noticeable, but when you do, you'll laugh hard. Watch this video at the 1:13 mark. Watch how the Doctor "covers" himself when he realizes he's naked.
That scene when the Doctor talks down to the footballer with his whole "Oncoming Storm" shtick like he was a Dalek or something, before realising that "annihilate" was figurative.
The Doctor doing Craig's job, and being rude to an obnoxious customer. Including blowing a raspberry, and telling him to hold because "I need to eat a biscuit".
The exchange near the end would be dramatic, if it wasn't for this line:
Craig: Will it work?! The Doctor: Yes! Craig: Are you sure?! The Doctor:Yes! Craig: Is that a lie?! The Doctor: OF COURSE IT'S A LIE!!
Also in the behind the scenes Confidential of that episode, any time the football show was recapping the match between the pubs like it was a real game, with actual logos and idents and everything. The BBC must have had fun with that one.
A meta one, but if you watch this episode on Amazon, when the Doctor is talking to the cat, it very clearly, very angrily growls. The subtitle for the episode say "(CAT PURRING)".
River escaping from her Cardboard Prison using her hallucinogenic lipstick, complete with a stick figure doodle and a note on her cell wall saying "Bye!"
River goes to Dorium Maldovar for a time travel device. He says they're not cheap, and she offers a device that can disarm micro explosives, like the ones she put in his wine. His expression is not angry or scared, it's annoyed.
What are the legendary first words of recorded history? The message from the dawn of time written into a mountain made of diamond? "Hello Sweetie" in fifty foot letters.
The Doctor: You graffitied the oldest cliff face in the universe. River:You wouldn't answer your phone!
Amy's favorite subject at school: Invasion of the hot Italians.
Amy: Yeah, I did get marked down for the title.
How to deal with a Cyber-arm:
The Doctor: You know how I sometimes have really brilliant ideas? Amy: Yes... The Doctor: Sorry. [runs out from under cover]LOOK AT ME I'M A TARGET!
The thumbs up exchange between the Doctor and Amy: the Doctor has this big goofy smile, while Amy looks freaked out as all hell.
The Doctor's extremely delayed reaction to the re-appearance of Rory.
The Doctor: I'm missing something obvious here, Rory. Something big, something right, slap bang in front of me! Rory: Yeah, I think you probably are... The Doctor: Oh, I'll get it in a minute.
That he first leaves the room, then when he comes back in walks up and pokes Rory's chest, then he sloooowly rocks back, then back forward complete with creaking noises from his armour is the icing on the cake. Then the following occurs:
Rory: Hello. The Doctor:[looong pause] How've you been? Rory: Good. Yeah, good. I mean ... Roman.
As Rory and the Doctor are talking, the Doctor throws up his hands and looks like he wants to scream "what the fuuuuuuuck?!?!"
"I don't mean to be rude, but... you died!" "Yyyyeah. I know. I was there."
The bit where the Doctor's interrogating Rory about his death.
Rory: It's all a bit fuzzy. The Doctor: Fuzzy? Rory: I died and turned into a Roman, it's very distracting.
The Doctor's hyperactive hopping about through time with a mop AND WEARING A FEZ!
Just before vanishing, the Doctor warns Rory to stay out of no doubt making Rory spend a couple of millennia worrying about what the rest of the sentence was. It turns out to be "trouble".
What Future Doctor tells Rory: "Rory, listen, she (Amy) is not dead. Well, she is dead, but it's not the end of the world. Well, it is the end of the world..."
Also, the younger Doctor not believing that he will give Rory his sonic screwdriver is quite funny as well.
Anything involving that fez, especially its destruction at the hands of River and Amy.
Speaking of the fez:
Beth Willis: Steven mentioned the fez to Piers and I before he even wrote it. He said, "Im thinking of putting Matt in a fez in episode 13." And of course Piers' and my jaws hit the floor and went "A fez? Youre kidding me, youre going to put Matt in a fez? If we put Matt in a fez Matt will never take the fez off. He will want to wear the fez for the rest of the whole series. It will be glued to his head. Hell be wearing it, you know, with his own clothes. It will be a nightmare." He said, "No no, Ive got a cunning plan; as soon as hes got the fez Im going to kill the fez."
The Doctor's reaction to Amy and Rory reuniting and kissing each other after Rory stuns the Dalek attacking the Doctor and the two Amys was hilarious.
The Doctor: And break! And breathe!
Rory calls Amy while brushing his teeth. She asks if he feels like there's something he's forgetting, something huge that's left an empty space in his head where it should be. He thinks for a minute or, rather, checks and then goes "yup" in the most matter-of-fact manner possible.
Amy: Are you just saying "yep" because you're scared of me? Rory: Yep. Amy: I love you. Rory: Yep. I mean, I love you too...
Amy calls the Doctor on being late for her wedding, then thinks she's finally surprised him... Good thing the Doctor just happened to be wearing a wedding-appropriate suit.
The look on Rory's face as he says the second part of the line just seals the funniness:
Rory: It's the Doctor. How did we forget the Doctor?
Rory: No! I'm not Mr. Pond! That's not how it works. The Doctor: Yeah, it is. Rory: ...yeah, it is.
The Doctor dancing like a monkey at Amy and Rory's wedding, and being copied by a crowd of children. That was all Matt. The only clue script-wise towards the Doctor dancing was that Amy calls it terrible and embarrassing.
And the ending, when the Doctor is trying to sneak out...
Amy: Oi! Where are you off to? We haven't even had a snog in the shrubbery yet. Rory:[following her into the TARDIS] Amy! Amy: Shut up, it's my wedding! Rory:Our! Wedding!
"And what sort of time do you call this?" Yes, folks, River Song makes a timing joke... in a world where time literally doesn't move!