Issue 11 of Doctor Who Ongoing has a Freaky Friday plot in which Amy and the Eleventh Doctor get swapped. Rory doesn't care what Amy looks like. At the end, not knowing that they've just switched back, he declares this and says they'll make it work just before passionately kissing the Doctor. Amy says they should do it again, but slower.
Doctor: An android! A positively spendid android! What do you have in here, a positronic brain? Those can be tricky to untangle, need lots of artificial synapse jumping. Looks like you've got it running very smoothly. Data: Curious... Riker: Um... Amy: Doctor, you're being rude! Doctor: Top-notch workmanship, I have to say. Did you build him yourself? Data: Please let go of my head.
Jonathan Pryce's gloriously OTT Master is a Crowning Villain of Funny. The Evil Laugh that causes thunder and lightning to strike while he's inside his TARDIS? The Dalek control "bumps"? His cybernetic upgrade (his hand's been replaced by a plunger)? And he is NOT CAMP!
The female Doctor, inspecting her sonic screwdriver: "Ooh, look—it's got three settings!"
After the Doctor explains how he'll tell the Master that the Daleks are planning to screw him overnote The aliens communicate by breaking wind:
Emma: ...Can I be tied to a different chair? Dalek: Si-lence. Emma: ...Why do you have chairs on a Dalek spaceship anyway? Dalek: ...We will ex-plain la-ter.
Heck, every time they need to say I/ We will explain later.
The Weakest Link Special
The very fact that K-9 is a contestant. No, not his voice actor, K-9 himself.
Then, at the end of the first round, everyone votes for K-9 as the Weakest Link. Even K-9 himself, who said "K-9" when the answer on his podium said "Andrew". This was actually a deliberate choice to eliminate the tin dog first because K-9 props just have the worst track record of breaking down out of nowhere and they didn't want to chance it in-game.
The three Doctors trying to call Tom Baker. Nobody wants to do it at first, but Colin Baker finally calls him, and his voice mail says he's not available because he's been sucked into the Time Vortex. Again. Made better because they used the same footage that was used in the original Five Doctors (taken from unfinished story "Shada") when Tom Baker had refused to do that as well.
Peter Davison and his dream about the Doctor Who production team — including Matt Smith and Steven Moffat — welcoming him to the studio.
Jenna-Louise Coleman warmly assures Peter Davison that he was her mum's favourite Doctor. One double-take stink-eye later, she amends it to her favourite Doctor.
Who else should snap him out of his dream but Tegan herself, Janet Fielding?
Sylvester McCoy and his constant bragging about being in The Hobbit. This culminates in a cameo by Peter Jackson and Ian McKellen (in full Gandalf gear), the latter initially having trouble remembering who Sylvester is, before deciding to do his scene without him, because it'll probably be better that way.
The description of Sylvester/Radagast: "Little bloke, bird poo..."
Gets even funnier when you listen to behind-the-scenes for "The Light at the End", which makes it appear that he is really like that. First, he says that he had the luck of playing three great roles in his life: the Doctor, the Fool in King Lear, and Radagast. He then proceeds to explain how he got the role of Radagast (starting with how he was considered for Bilbo in LotR). When they start talking about stamps made with all of the Doctors, he says that he is on two different stamps, since there is a Radagast stamp in New Zealand.
Colin Baker forcing his family to watch one of his old episodes with him, which he bought to replace the copy that "mysteriously" got destroyed.
Colin: You're wasting your time. I've locked all the doors!
Also the Brick Joke to his earlier complaint that there's no reception at the bottom of his garden, cutting to him randomly standing on a tractor.
David Tennant appears and gets a phone call from his wife. She asks him to help out her dad — Peter Davison — while she's in the hospital about to have her baby. David hangs up on her and completely forgets to ask about his kid.
In an earlier scene, Pregnant!Georgia is seen eating a stick of celery dunked in chocolate ice cream.
How about Peter Davison's sons being totally thrilled their brother-in-law David will probably be in the special — and when they realize their father won't be in it, they're even happier!
John Barrowman driving the three old Doctors to Cardiff and singing Broadway tunes all the way there. When they get out of the car, he throws them each a John Barrowman CD which they use as payment to get into the Doctor Who Experience exhibition.
What clinches it is the fact that the receptionists have a box full of them.
The fact that they get the lift by blackmailing John Barrowman after learning his awful Dark Secret — he's straight, married and has kids.
Earlier, John Barrowman snarking at their picketing at BBC Television Centre by pointing out that the new series is filmed in Cardiff.
And before John gets there, Colin Baker and Sylvester McCoy are drinking tea, while Peter Davison stands there with a sign, and they have this little side exchange:
Sylvester: Ah, yes. A decision. Thank you...will it make a difference?
Sylvester: Every great decision creates ripples.
Colin: In your tea?
Sylvester: Like a big boulder dropping into a lake.
Colin: Sylvester, if you don't stop quoting yourself I'll put you back on the plane myself.
Sylvester: And what the heck are those things? Have they turned it into a helicopter?
Culminating in Peter Davison complaining about how the new sets are actually built to be sturdy.
Peter: And look at this, look! You lean on it and nothing happens! It doesn't wobble at all! I used to love the old wobble!
The same three disguising themselves as Daleks to get into the 50th anniversary special. At the end of the short film, Steven Moffat cuts all the footage of those Daleks from the special.
When the three are escaping from the studio, an angry assistant - mistaking them for the Dalek operators - tells them they have to stay to play the Zygons. Peter Davison turns around and says "Sorry, must dash!" and then looks immensely proud of himself.
Then in a mid-credits scene, we learn they ended up becoming the shrouded Zygons in the Under Gallery.
The very fact that Steven Moffat appeared in the special at all is kind of a Crowning Moment Of Awesome, at least because he's not ignoring the older Doctors entirely and is perfectly willing to poke fun at himself.
Steven Moffat looking like he's busy writing, only for the camera to pan out and reveal he's actually playing with figurines of the Tenth and Eleventh Doctors.
The very beginning, where Sean Pertwee and Olivia Colman compare their very prestigious upcoming projects, only to start complaining about how they couldn't even get a look-in to participate in The Five(ish) Doctors Reboot:
Olivia Colman: I'm usually in everything!
After cramping themselves into the fake TARDIS prop, causing Peter to become confused why they didn't end up in the "real" TARDIS, Sylvester adopts an expression that makes it clear he thinks Peter has gone absolutely insane.
Sylvester: (Worried) I think I want to go home now.
Slightly before Sylvester chimes in, Colin says to Peter with a look of complete incredulity:
Colin: You really are from another planet, you know that?
One of the security guards on the set refers to Sylvester, Colin and Peter as "illegal aliens".
The reveal that Paul McGann and Russell T Davies are similarly badgering people to get involved in the anniversary and the Five(ish) Doctors Special. The latter's voice mail to Peter containing various pitches for his cameo lasts over 27 minutes.
Even better, McGann seemingly disappears after having one scene, despite being listed in the main titles, due to filming commitments. The other Doctors don't know just what filming commitment he has, but the audience does: The Night of the Doctor! And in keeping with the tone of the movie, of course he doesn't tell them!
Steven Moffat has a nightmare about floating heads of all the previous companions nagging him about appearing in the anniversary. It culminates in Matthew Waterhouse (Adric) popping up and asking gleefully "It's me, isn't it?!" The floating heads all explode, causing Matthew to go "Now I'll never know if I was right!".
As they're breaking into the studio, one of the Dalek props turns to look at them as they walk past.
More Dalek prop humor, when the production assistant is haranguing the Dalek!Doctors, asking them if they understand how lucky they are, and what an honor it is to appear in the episode; the Doctors look at each other and then silently nod their eye-stalks.
When Jenna-Louise Coleman was having her first interview after it was announced that she'd be the next Companion, she was asked her favorite monster and she replied, "I'm pretty sure I'll run into the Daleks at some point." A bit of Hilarious in Hindsight deliberately invoked by Jenna, since she definitely already knew (and had possibly already filmed it) that in her first episode, she'd be playing a human turned into a Dalek, 5 episodes and 3 months before anyone was expecting to see her on the show.
The entire cast and crew of the Davies/Tennant era performing The Proclaimers' "500 Miles" at the wrap party for "The End of Time". I dare you not to laugh at the sight of an Ood dancing.
After the word got out that a warehouse in America accidentally sent out the Series 7b DVD a little too early (as in, before the finale aired), the BBC and other assorted Powers That Be all politely asked that the fans who received them not spoil anything for the rest. Whovians responded in their own unique way, namely by spamming the post with so much insane nonsense that even if the truth were revealed (which it wasn't, by the way) they wouldn't believe it anyway.
For the 50th anniversary of the show, the official Twitter put an image with the phrase "On this day [September 19] 50 years ago, filming began on a new BBC TV Series called Doctor Who…". The fans' response? "It will never catch on."
Chris Hardwick: From a scientific standpoint, everything she's doing should not work. And yet it is. — Matt Smith: Karen's got the highest score! Chris Hardwick: SHE DOES HAVE THE HIGHEST SCORE. *hangs head in shame*
Matt and Arthur poke fun at this, affectionately agreeing to call Karen "an idiot", to which Karen gets adorably defensive.
Chris Hardwick's TARDIS ball.
Chris Hardwick: It came through a tear in the fabric of the universe. Or I just paid a hundred bucks and had this printed onto a ball. With a laser, so that's kinda sciencey.
Matt Smith being absolutely terrible, to the point where he has a counter for the number of pins he's hit (his final total seemed to be roughly 16, which a competent bowler can make in two turns.)
Steven Moffat: What you need to do is try to hit some of the pins. — Matt Smith: I've got one pin! I'm the worst in the game! Karen Gillan: Hahahaha, one pin! Matt Smith: Shut up, Karen.
Steven Moffat wasn't much better; in several frames the ball would arc through the air and only land about halfway down the lane. One of the other guys said he throws the ball like a caveman and should probably switch to softball. Notice that Moffat's competitiveness still came through, lasering in on the fact that he was at least better than somebody, namely Matt, who he teased mercilessly about it.
Arthur Darvill is so "fluid" when swinging his bowling ball (using just about his whole body to throw it) that Karen jokes that he "has no bones".
Karen Gillan: Come on, Arthur! Show them what you're made of! Arthur Darvill: I'm not really made of very much.
We have no knowledge of the black archive at the Tower of London. Then again, we might have had our memories wiped
During the 50th anniversary of the series, multiple live celebrations were going on. Ironically, Doctor Who Afterparty, the one with the main cast members of the special, executive producer of the special Steven Moffat, and many prominent classic series stars, went completely Off the Rails. They decided to do an interview with One Direction over their live feed, who had declared the same day as the anniversary "1DDAY" and were performing a 24-hour livestream. Someone got the crazy idea this was to rival the series, when OD was an American band having next to nothing to do with the series, and it was merely an accidental coincidence. This livestream linkup could have worked in both the band's and DW's popularity favor... except that there was a delay between transmissions on either side. It promptly turned into a massive farce that will go down in Doctor Who infamy even more than Dimensions in Time.
Steven Moffat: In the name of God, we can't do this!!
Matt Smith also appeared to flick the V at One Direction. In America, the gesture can be seen as inoffensive, but in Britain... it means "piss off".
"This is my Timey Wimey Detector. Goes ding when there's stuff."