Clara is saying the Doctor she knows will come for her no matter what, holding out a hand waiting...and then a hand moves into hers and pulls her back. One of the "robots" peels off his face to show the Doctor just as his new theme music kicks in.
The Doctor: Hello, hello! Rubbish robots from the dawn of time!
Clara's refusal of the Half-Faced Man's demand. Added points for the fact that Clara is visibly terrified and crying while doing so, yet never backs down. Lampshaded by the Doctor:
The Doctor: Five-one and crying. You never stood a chance.
Jenny and Vastra make a very stylish Big Damn Heroes entrance into the "larder" of the ancient ship.
Vastra:Remain still and lay down your weapons in the name of the British Empire!
The Doctor's final confrontation with the Half-Faced Man. He tells him he's afraid he's going to have to kill him, surmising it's the only way to stop him and that he's the command module for the other clockwork droids. After a brief scuffle, in which the Half-Faced Man says he can't self-terminate and the Doctor says he can't kill him, the Doctor says one of them is lying. Cue the Half-Faced Man impaled on a tower, and the Doctor giving the camera a hell of a Death Glare.
The Doctor: Those people down there? They're never small to me. Do not make assumptions about how far I will go to protect them, because I've already come a very long way! And unlike you... I do not expect to reach the Promised Land.
The Doctor gets one not only for rescuing Journey at the last second, but when she's threatening him with a gun, he doesn't bat an eye or even put his coffee down. He just calmly tells her that that is not how you ask for something. He actually gets her to back down and ask for help politely.
Despite being a Pyrrhic Victory on the Doctor's part, Rusty the Dalek turning on and destroying the rest of the Daleks is admittedly pretty spectacular.
Rusty:I see into your soul, Doctor. I see beauty. I see divinity. I... see... hatred! ... I see your hatred of the Daleks, and it is good!
This episode captures the true horror of a Dalek assault force. A Dalek saucer descends on to the Aristotle, which is dwarfed by the saucer's size, with cries of "Exterminate" echoing all around. Chillingly awesome.
Likewise, the Combined Galactic Resistance deciding that, if the Daleks want to take down the Aristotle, they're going to have to fight through them to achieve it.
Colonel Morgan Blue: That door's never going to hold. But I'm damned if I'm going to make it easy for them!
After Robin Hood attempts to steal the TARDIS, all property being theft to him, the Doctor defeats him in a swordfight with a spoon.
Robin vs. The Sheriff. It starts with a sword fight and ends with Robin copying the Doctor's evasion technique to knock him into the gold vat.
The Doctor leading the enslaved peasants to revolt against their captors. They take unmelted gold plates and use them as reflector shields against the robot knights' laser beams. The Plan is so successful that all of the robots in charge of the area are completely destroyed, allowing the peasants to escape.
Robin managing to shoot a golden arrow, as in an arrow that must weigh more than a brick, miles into the air with an 1190-ish bow. With his arm broken! While compensating for the two other people who are helping to hold his bow!
"When did you start believing in impossible heroes?" The fact that Robin Hood was so impossibly awesome that each and every one of the Doctor's regenerations believed it couldn't be real. Not even the child-like Eleven or the human-curious One ever considered him plausible enough to even investigate. Coming from someone like the Doctor, that says a lot about how awesome Robin is.
Clara: Promise me you won't look at where we've been. Just fly us out of here. The Doctor: I don't take orders, Clara. Not from anyone. Clara:Do as you're told.
The Doctor turning his back on the monster under Rupert's bed, and then urging Clara and Rupert to do so with him. Sure, he was terrified for their safety if they saw something that evolved to be a perfect hider, but it takes true courage to ignore the things you're scared of if it means protecting someone else.
Really, the whole heist is one for the Doctor. He puts together the perfect team and makes it through the biggest, most impenetrable bank in the universe, all to save the lives of the last two of an ancient species.
Quell: What kind of soldier would I be to die with bullets still in my gun?
The Doctor lives up to his earlier Badass Boast; "One minute with me and this thing would be over."
The villain of the piece manages to be smart enough to get all the information they needed, blew up the train to prevent the Doctor from finding them, and is still out there somewhere, having gotten away scot-free.
Foxes contributes an incredible slow-jazz cover of "Don't Stop Me Now".
The Doctor, trapped in a tiny TARDIS, escapes from the path of an oncoming train, by reaching through the door, lifting the TARDIS from the outside and walking it off the tracks like the Thing from The Addams Family.
Clara using the Boneless' powers against them to get the TARDIS back to normal.
The Doctor's speech to the Boneless as he banishes them back to their home dimension after regaining control of the TARDIS.
The Doctor: I tried to talk, I want you to remember that. I tried to reach out, I tried to understand you, but I think that you understand us perfectly. And I think that you just don't care! And I don't know whether you are here to invade, infiltrate or just replace us. I don't suppose it really matters now, you are monsters! That is the role you seem determined to play, so it seems that I must play mine! The man that stops the monsters! I'm sending you back to your own dimension. Who knows? Some of you may even survive the trip, and if you do, remember this: you are not welcome here! This plane is protected! I am the Doctor! [catches his screwdriver] And I name you: the Boneless!
Missy, for elegantly setting up a plan behind the Doctor's back, hiding her true identity from him, gathering countless cadavers to build up the Cybermen armies, and reaching the point of victory in one fell swoop.
Her reveal as well should get special credit:
The Doctor: Who are you? Missy: Oh, you know who I am. I'm Missy! The Doctor: Who's Missy? Missy: Please, try to keep up. It's short for "Mistress". Well... Couldn't very well keep calling myself "The Master", now could I?
Missy basically conquers the world, and can easily conquer the universe by pushing a button. The only reason she loses is because she wants the Doctor to be her friend again so much she basically hands the Doctor a win switch, knowing he doesn't dare use it without giving her what she wants. On top of that, she flummoxes the Doctor so much that this almost works. The Doctor, even when he prepares to kill her, flat out admits that she won.
A posthumous one for an old friend. Even in death, at the Earth's darkest hour, the Brigadier defended his world one last time, by shooting Missy, and saving his daughter after she fell out of a plane. Plus, it gave the Doctor a second chance to say goodbye after he missed out the first time, and let Twelve do the one thing Three never did: Salute his old friend.
After being blown out of Base One, the Doctor proceeds to skydive into his likewise descending TARDIS.
The Doctor, faced with a Sadistic Choice accept Missy's army and use it to conquer, or allow the Cyber-Rain to wipe out humanity - does what he does best, Takes a Third Option, giving control of the Cyber-Army to Danny. All because the Doctor sees that he was wrong, that Cyber-Danny won't harm Clara and that Heart Is an Awesome Power.