Best of lists always create antagonism (unless the list in question is this year's Turner or Walters prize finalists, both of which have pretty much disappeared without creating a ripple).
These lists of the Best Children's Books Ever by Lucy Mangan for The Guardian certainly raised ire as well as endorsement in the comments section. But debate's part of the fun, right? Why pick Matilda over Danny, Champion of the World (or Boy) - and so on, and so on.
I can't speak for the books for wee kids, but I think the lists for 8-12 and 12 and over are real gems. I particularly like the way recent books (Patrick Ness's Chaos Walking trilogy, for example) are mixed with the often-snobbishly-overlooked (come on, what girl didn't feel secretly relieved upon reading Are you there God? It's me, Margaret) and the classics - The Borrowers, I Capture the Castle.
Sure, if I were including a saccharine morality tale for girls I might have gone for A Little Princess over Little Women (only because I still resent Jo's decision - why, Jo? For the love of god, WHY?) . I would have liked to see either Ursula Le Guin or Madeleine L'Engle in there. And naturally, I'm pissed that The Sword in the Stone - hands down best children's book ever - doesn't feature. But nonetheless, you should check the lists out.