The scene where William comes to meet Emma at the Maulders' manor. When she sees him coming, the normally calm Emma drops everything and rushes straight out the front door into his arms (surprising the HELL out of the rest of the staff).
The wedding of Emma and William at the end; the entire chapter just oozes heartwarming.
Most especially, the fact that Heinrich was happy to give Emma away to William in place of her father.
Several of the side chapters featured them, most notably 'Dreams of Crystal Palace' which covered one of the happiest days of Kelly Stownar's life, visiting the Great Exhibition with her late husband.
The scene were Emma reveals to Kelly Stowner the necklace that she had fixed which had been broken, knowing how important it was to her mistress and the woman who had taken her in. The appreciation and amazement on Kelly's face on seeing it as new, in how Emma had used the photo of her and her husband as reference.
Then, in thanks, Kelly gives the necklace to Emma for her to have since she is still young and can better put it to use.