I love the questions, even though usually my answers involve something like, "Here's what some people believe, and here is what others believe." OR "Let's look that up on the Internet!"
My favorites have been about how animals evolve - DD4 is very interested in paleontology and archaeology, and we've done everything from mock digs in the backyard to reading everything we can get our hands on. Related to this are the countless questions on Human Growth and Development in utero.
DD4 is also interested in the idea of God - her preschool teachers make the kids pray before lunch, and she can't figure this out. "Mom, why do I have to thank someone that's invisible for lunch? You made my lunch, so I decided to thank you instead." And, "My teacher told me God lives in the sky. But I know that clouds are just water vaper, so that can't be true. He'd fall right through!!"
I think we have a budding skeptic on our hands.... :-)