Alphonse's reaction when he finds out that Edward is getting married.
Roy and Riza's subtle but meaningful conversation in Chapter 3:
"You equate protection with love, Colonel?"
She doesn't know what the right answer is, because to lie goes against everything she's ever stood for but to tell the truth is entirely too honest for them. She tries, therefore, for something in the middle.
"When the protection extends as far as Edward is willing to protect Winry, sir - with all of his being, to shield her from every conceivable harm to her person and her heart and her soul - then yes, I would venture to say they are the same."
He nods, as though this is exactly what he expected her to say.
Edward's explanation of a chimera to Winry in Chapter 5 which is so ridiculous it crosses over with a Crowning Moment of Funny:
Edward: "A chimera is what you get when you get two life forms and more or less merge them into one being."
Winry: "That sounds revolting."
Edward: "It can be - but if you think about it, isn't that what we're doing?"
Winry: "I don't follow."
Edward: "We're taking a you and merging it with a me and the result is going to be an us. And the us will be better and more complete than the you and the me were by ourselves. A chimera."
The Team Mustang reunion in Chapter 6.
Riza's promise to Winry:
"You asked me why I was a soldier. I told you that it's because there's someone I need to protect, and you seemed to understand that. Well, starting right now, I have two people I need to protect." Obeying some maternal instinct, she brushes hair out of Winry's eyes. "I will bring him back safely. All right?"
The Game of Three Generals
When Roy is put on trial for the murder of Fuhrer Grumman we get this exchange.
Prosecutor: Well, maybe you love your ambition more than you love your wife.
Roy:I don't loveanythingmore than my wife.
Izumi's conversation with May in the second chapter, particularly the idea that Hohenheim and Trisha are looking after the son she lost in return for her looking after Ed and Al.