So someone posted a still of this part of the scene, but seeing this in a gif made me realize, just how long Emma is staring at Neal.
I think she is starting to realize that he went through so much more than he ever let on, and that he is so much more heroic and good than she ever thought. He never tried to use his past as an excuse or to justify what he did. He doesn’t try to take credit for things, let alone things he didn’t really do. He apologizes for his mistakes. All the good things she ever saw in him are still there, but she now has reasons to second guess the bad things she imagined he must be like to have left her the way he did. Right now, all she can handle really is making sure they get Henry back, but she is seeing him in a new light, and she cannot stop looking!
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass