In the sequel, as Nanny McPhee leaves, the children's dad returns. Especially heartwarming, considering that she only leaves when they do not need her anymore, and they truly don't: Their family is back together again.
Not to mention, the father hugs his niece and nephew and is just as happy to see them as his own children. Compare this to their own father, whose idea of a heartwarming reconciliation is a firm handshake, and it's incredibly sweet.
In the first movie, the whole ending was Heartwarming especially with Nanny McPhee nodding to the mother's chair in the study.
In the sequel, we see that the children Nanny McPhee raised not only remember her, but pretty much squee when they see her again. A stoic guard in London breaks down in Tears of Joy at the sight of her and admits that he can't lie when she asks him if he still eats his vegetables, and we find out that Baby Aggie from the first movie, even all grown up and forgetful, is happy to give Nanny McPhee a place to stay.
Nanny McPhee taking the kids to the beach in the first movie, using her magic to untangle one of the boys' kite strings and calling him sweetheart.