When people ask me how to understand the deep internals of Unix I always recommend this book.
http://www.amazon.com/dp/0201702452/tomontime-20
Even if they use Linux instead of *BSD, this book is the best way to learn OS internals and... well... 90% of it applies to Linux.
Many years later, has anyone written a Linux equivalent?
I have a book on Linux which includes the v0.x? source code and a commentary. It's at my other office, so I can't grok the title nor author. It's styled like the classic John Lions books for Unix which of course was the inspiration for Linux.