He suspects he might be in trouble the first time he takes her into the TARDIS and she immediately starts pushing buttons she's not supposed to, without even asking, will this kill us? Other companions have stared, asked questions, hovered, even run away. Some people are so afraid of breaking something or accidentally blowing up the whole machine that they ask permission every time before even leaning on the console.
Amelia Pond walks in and starts pushing buttons.
Ooh, thinks the Doctor, this is gonna be good.
He feels incredibly…he doesn't even know, when she refuses to take back a single word, and instead tells him that she knew, even though she couldn't have, he knows she couldn't have. Very old, and very kind, and the very very last. Sound a bit familiar? He wants to tell her she's still wrong, she still shouldn't have done what she did, and he's oh so much more complicated than that, and she shouldn't even try to understand him. No one ever quite understands him—they are intimidated by him, or filled with fear, or with too much respect, or with hatred.
Amelia Pond looks straight at him and spells out his soul.
Damn, he thinks. But he has to hug her. He couldn't do anything else.
He thinks he might be in love when he and Amy have their feet up on the TARDIS console, filling in the bits and pieces of what will later be known as "the Churchill fiasco," and she mentions that going to Bracewell for the alien tech was her idea, that she was the person who said "gravity bubble" and "send something up there." He stares at her. That's twice now that she's saved the whole of humanity, just today.
Amelia Pond is…he doesn't even know.
He has to restrain himself from jumping up and kissing her again.
He knows he's in love when the stone angels are closing in around them and Amy's stone-not-really-stone hand is clenched on the railing and she's begging him to leave her there, not because she wants to die, not because she just wants him to live, but because she can't help but put the lives of other people, complete strangers, before her own. It's the only natural reaction she could have. He's been in loads of "I'm not leaving you" situations before, but they've always been tinged with selfishness, with concern for the Doctor himself. She looks past him into the darkness of the catacombs and asks him to save the others.
Amelia Pond is…magnificent.
There's the word he was looking for.