My reasons for suggesting these is that each one is child friendly or aimed at children. I loved all of these as a child and I think they helped me develop my sense of empathy.
Animorphs (the books not the TV show). It's a wonderful series for children, at least I thought so when they came out. I believe it's actually being updated and rereleased. It's about a group of friends who find a dying alien Prince who tells them their world is being invaded and gives them the ability to turn into whatever animal they touch. I credit this with my love of biology and wildlife.
Prehistoric Park. Walking with Dinosaurs/Beasts/Monsters/Cavemen and whatever else they have. Reasons should be obvious.
Doctor Who. This is something that has such a dedicated following from people around the world, huge numbers of fans both religious and non religious alike. Far as I can tell the Doctor is an atheist who shows a huge range of themes, dealing with the religious (at one point actually meeting the Devil and denying said Devil's existence) tolerance of others and the important of morality, learning and being wrong that is often completely void of religion yet so easy for everyone to identify with.
X-Men series from the 90s. I remember when this first came out and was captivated by it. It deals with racism, prejudice and the struggle for equal rights in a way for a child to understand. I was around five when I watched this and I still remember the impact of hearing Storm talk about how people fear what they don't understand and how different can be dangerous.
The Magic of Reality by Richard Dawkins. Came out recently. Got this for my sister's 9th birthday, fascinating read. Try and get the illustrated version, the drawings are pretty
It may be a little beyond grasping at that age but if you read it yourself you'd find it simple to explain things to your children. It involves the evolution of life, where humanity came from, different religious creation myths and why some people don't have a religion, the importance of learning new things and is just a fascinating read. I would seriously advice it.
So, with the last as an exception, just my two cents from what I remember about things opening my own mind as a child.