2. The Impossible Girl And The Clever Boy
The Name of the Doctor basically sealed the deal on this question for me. First there was the conference call, in which the Doctors dead wife and current companion were referred to as the women by Madame Vastra. When Vastra tried to introduce Clara, she ended up stumbling over her own tongue and turning a darker shade of green.
Keep in mind that, the last time we saw River, she urged the Doctor to find a new full-time companion. So, why exactly is she making this face?
Clara finds the whole thing bemusing, because apparently the Doctor forgot to mention the whole dead wife thing (to her or us). Not only that, but somehow Clara ended up with the impression that Professor Song was a man.
Later, Clara asks the Doctor who River was, referring to her as the lady with the funny name and the space hair. When the Doctor says yes an ex, Clara makes this face, so quickly you probably missed it:
So, Clara, hows that dont fall in love plan working out? Fast forward to the inside of the Doctors tomb. Clara freaks out about the Doctors crisis way more than his other friends
And proceeds to jump into the Doctors time stream, knowing itll kill her, without any hope of rescue. She goes knowing that shell die not just once but many, many times. He literally begs her not to, shouting her name as she walks further away, and again even after she's gone. But she decides to do it anyway, because its the only way to save the Doctor. If thats not an act of love, I dont know what is. And even though its both impossible and unbelievably stupid, the Doctor goes after her. He says an (apparently) final goodbye to his wife, and goes to get Clara, (her advantage over the Great Intelligence being shes got me) whom hes suddenly taken to calling my impossible girl.