The Amy Code
Amelia Pond has never been much for showing affection. Yes, she can flirt outrageously, kiss the socks off a man when she feels like it, and generally drive him crazy in exciting ways – but showing her true feelings is another matter. She does that in subtle, roundabout ways that most people wouldn't even notice, as if she were afraid that being too open would scare them into leaving. Since he met her, the Amy Code (as he privately thinks of it) has taken Rory Williams years to figure out.
A punch on the shoulder means reassurance: I knew I'd be coming back, she'd said in the alleyway in Venice, avoiding the question of whether she had missed him. Ruffling his hair means remembering a lifetime of familiarity: You could be my brother (although that really wasn't what he had in mind).
There is a certain smile she shows him, bright and twinkly and irresistible, that means she is about to get them both in trouble (just like in high school when they were caught making out on the rooftop). He would always take the trouble for the sake of that smile.
Also, he is probably the only man in the world who likes being called different variations of "stupid" by his wife. It's the strangest and most important code word of all, which no one who does not know her could possibly understand.
Amy knows quite well that Rory is not stupid. She encouraged him to get through his training as a nurse, helped him study for his exams, brags to her friends that she has a fiançé who saves lives, and shows her ferocious ginger temper to anyone who suggests that nursing is an unmanly profession. The only times she uses that word are either when he doubts their relationship (I've already chosen – it's you, stupid!) or when one of them is in danger.
After saving him from the vampire-alien-fish Francesco, whom he'd attempted to fight with folklore and a broomstick: Why'd you make the sign of the cross, you numpty? Followed by an epic kiss on the staircase which left him literally dizzy.
Listening to her recorded voice after she was abducted by the Silence: I love you … I know you think it's him, I know you think it ought to be him … but it's you. My life was so boring before you just … dropped out of the sky. If we live through this, I'm gonna tell you properly … just to see your stupid face. At the time, sitting next to the Doctor with the little red recorder in his hand, Rory felt painfully uncertain about the addressee of that speech of Amy's. "Dropped out of the sky"was so suggestive of the TARDIS, not to mention their life in Leadworth being boring … it was a complaint she'd made more often than he could count. But then again, she had never called the Doctor stupid before, had she? Perhaps because he is simply too much of a brilliant, heroic Time Lord for even Amy to apply that epithet. Or perhaps because he wouldn't understand.
Get your stupid face out of here! That was the moment Rory knew. It's a subconscious thing – the same words, the same thoughts, repeating in her mind. "Stupid face" means: "It's stupid for you to put yourself in danger". It means: "I need you to be safe". It means: "I love you."
"I'm never gonna stop being stupid!" he tells her, swirling her around in a delighted embrace.
Translation: "I love you too".