Rufus's flashback to when he last saw Penny, alone on her bed, sad because she wasn't adopted, and comforts her with his "Faith is a Bluebird" poem. The music that plays in this scene is also tear jerking. As is Penny saying "I love you, Rufus" while petting the grandfatherly cat.
If 'Faith is a Bluebird' doesn't make you tear up a little...
Faith is a bluebird you see from afar.
It's for real, and as true as the first evening star.
You can't touch it, or buy it, or wrap it up tight;
But it's there just the same, making things turn out right.
The "Tomorrow is Another Day" montage.
Miss Bianca cuddling up with Bernard on their way to Louisiana.
Penny praying, not only for herself, but for her teddy, Rufus, and all the kids at her orphanage, and that she and they will all find happy homes and be adopted by new families.
The entirety of 'Someone's Waiting For You'. Some of the most gorgeous lyrics ever; not even necessarily the most poetic, but beautiful in their simplicity, and sung with an incredible amount of emotion.
Be brave, little one... make a wish for each sad little tear... hold your head up, though no one is near; someone's waiting for you...
Penny finally being adopted at the end, finding the loving home and parents she had longed so much for as her friends cheer them on.
Bernard trying to convince the Chairman that the mission is too dangerous for Miss Biana, and she is clearly touched by his concern. It goes to the next level when she chooses him to be her coagent instead of all of the others because he cares about her as a person, not just because she is beautiful and well-bred.