Oh this is a tough choice. I just watched the film, again, last night and the scene you mentioned, cherrios, when she closes the door so slowly because she wants to look at him for as long as possible is so so wonderful. My stomach does flips.
The scene in the rain where she does not accept his proposal is exquisite as well, as mentioned. The music when she is running across the bridge, how Mr. Darcy blabbers on then just says "I love you," when she doesn't understand and how his voice breaks is so heart breakingly beautiful. Then how the scene becomes one of their passionate fights is just perfect.
But my most favorite has to be the "You bewitched me body and soul.." scene because of simply, the way the sun pans in on them perfectly. I love how he stutters when he says "I love..I love...I love you" because it's so pure and then how Lizzie kisses his hands and just says "Your hands are cold." It's terribly romantic. And then the most intimate of gestures, more than a kiss, they just rest their foreheads on one another and close their guys, breathing each other in.
As you can tell, I'm a sucker for the romance in this film. Even yesterday, the ending kiss got me all choked up because Matthew conveyed Mr. Darcy's love for Lizzie so wonderfully.