"It's you."
"It's me."
"We better go. Shall we?"
Just seems to me like that the dialogue in that scene could have been written better. And then there's the odd way they stare at each other on the way to the elevator.
The whole scene is written to sum up the irony of what has been going on the entire movie. Sam is doing his best to avoid seeing or meeting Annie Reed, and Annie has been struggling to find a way to meet him because Jonah broke her heart with his story--a story is so sad I've seen guys wiping their eyes in the theater.
The looks are loving looks that are show how satisfied they are with the end result of what has been happening.