The top three are:
1) Charlotte's Web by E.B. White
2) A Wrinkle in Time by Madeleine L'Engle
3) Harry Potter and the Sorcerer's Stone by J.K. Rowling
I've read fewer than 20 books on this list, but the ones I've read probably belong there. These books include:
and the Harry Potter books. The only one I'd say doesn't belong there is the grossly overrated Alice in Wonderland.
Of course, I'd put them in a different order. My top 5 probably would look like this:
1) The Wonderful Wizard of Oz by L. Frank Baum
2) Anne of Green Gables by L.M. Montgomery
3) The Hobbit by J.R.R. Tolkien
4) Holes by Louis Sachar
5) Hatchet by Gary Paulsen
The Native aspect
Educator Debbie Reese reports that only one of the authors has any Native heritage. Wilson Rawls, who wrote Where the Red Fern Grows, said his mother was part Cherokee. He didn't claim to be Cherokee himself.
Reese probably would like to see several Native authors on the list. That may be unrealistic. Since Natives make up only 1% of the US population, getting one of the 100 slots would be fair. Rawls and maybe one other Native author would fill the Native "quota."
But as Reese goes on to note:
I say that in jest, of course, because most of those portrayals are in some way, stereotypical or biased. If you are a librarian, and you use this list to build your collection, you will not be providing your readers with a single worthy image of American Indians. A few of them are innocuous---like the Indian blanket in Charlotte's Web---but most are problematic. From "Honest Injun" to sitting "Indian style" to hunting Indians, there's a lot to say.
Reese lists many of these references. I'd say more of them are benign than Reese did. An Indian quiver, the plant known as Indian paintbrush, children playing cowboys and Indians...I'd call these innocuous, not problematic.
To be clear, I don't think kids should play cowboys and Indians, but it's a fact that they did and still do play it. I wouldn't put it in a book today, but in a book written 50 or 100 years ago, I don't consider it a problem. It's an accurate description of what children played then, not a conscious attempt to demonize Indians.
It appears three of the books--Island of the Blue Dolphins, Walk Two Moons, and The Indian in the Cupboard--are about Indians. All of these are problematic. So are Little House on the Prairie and its sequels. And others on the list have clearly problematic references.
Basically, there are no good books by or about Indians on the list. And few if any good books by or about other minorities, either. Whether the participants intended it or not, this is a white person's list of the best children's novels.
For more on the subject, see Portrayals of American Indians in SLJ's 2010 "Top 100 Children's Novels"--compiled by Elizabeth Bird--PART ONE and The Best Indian Books.