The Blue Flower by Penelope Fitzgerald
Almost any Penelope Fitzgerald novel could have served this purpose -- there are wonderful children in "The Beginning of Spring," "Offshore" and "At Freddie's" -- but I select this one not only because it is one of her greatest, but because it contains "the Bernhard," possibly my favorite character in all of her work, and certainly her most amazing child. Fitzgerald may well be the best novelist now writing in English; she is certainly unlike anyone else in her ability to create a time and place that is at once true to itself (18th century Germany, 1950s Italy, turn-of-the-century Russia) and at the same time utterly of a piece with her own marvelous sensibility.
The Child in Time by Ian McEwan
This is my favorite of McEwan's works, though "Enduring Love" (except for the end) runs a close second. It is the last of his works that features children and childhood -- after that, he turns to more adult forms of love and hate -- but it follows on the wonderfully creepy "The Cement Garden" and the evocative stories in "First Love, Last Rites." The main child in "The Child in Time" (other than a lost little girl) is a man who wishes he were still a boy, and pretends to be one.
Stories in an Almost Classical Mode by Harold Brodkey
People either love Brodkey's work or hate it, depending largely on whether they ever met Harold. I met him, and I still love it, at its best. Its best, in this collection, are the title story, "Ceil," and one or two others, all of which focus obsessively on his own childhood and adoptive family.
A Fine Balance by Rohinton Mistry
My favorite novel of the past few years -- not to be confused with the best novel, but carrying more of a tone of personal connection because it is a novel that hits you between the eyes, or in the stomach or wherever you are most likely to feel emotion. The children here are modified Dickens characters: modified to suit a modern sensibility, to make us able to feel strongly about them rather than merely wanting to escape their pathos.
So Long, See You Tomorrow by William F. Maxwell
Like Brodkey, but in the opposite way (wistful and modest rather than loud and boastful), Maxwell focuses obsessively on his own Midwestern childhood. Here, in a perfect little novel, he tells the story of a small-town murder from the point of view of a little boy who knew the child of the people involved.