The scene where Joanna is stoned by the jealous women and her baby winds up being hurt by it.
The scene where the children win a Christmas tree, and Johnny helps them bring it up the stairs and leads the entire building in a round of "O Holy Night".
The moment where Francie realizes that Lee has been playing her.
And how Katie handles it—when Francie addresses her as "mother" rather than "mama", she realizes that Francie has grown up and responds to her as another woman rather than as a child and doesn't condemn her when Francie reveals that she almost slept with Lee.
The scene (in the movie) where Francie and her mother reconcile as her mother is giving birth, especially when Francie reads her mother an essay she wrote about Johnny after he died.
The corresponding scene in the book is more straight tear-jerker than heartwarming moment; after ignoring Francie's writing for years, Katie finally asks to see some of it, only to find that she's recently burned it all. Katie is tormented by the understanding of how much of Francie's life she's missed out on by focusing on Neely—which still doesn't stop her from going back to her usual ways after the baby is born.
Francie's graduation, when she discovers flowers Johnny gave Sissy the money for before he died. Especially sad that Johnny did this knowing he might not be there for this special day.