Also take a look at the Sibert Medal, an award for exceptional non-fiction given by the American Library Association (which also gives out the Caldecott & Newbery Medals).
Outstanding Science Trade Books for Students K-12 offers detailed annotated lists for those who enjoy science.
Books for Boys (which is also great for girls, of course!) has a section with books organized by subject - just be careful, because some of these are fiction!
The Cooperative Children's Book Center has numerous reading lists, many of which focus on non-fiction. Select first by grade level, then by topic.