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Lions' Commentary on UNIX--With Source Code by John Lions, Peer-to-Peer Communications, Inc. This book is essential reading for anyone seriously studying operating systems. Even though it analyzes the kernel of a UNIX in use over 20 years ago, it still remains as valid as ever for educational purposes.
Modern Operating Systems by Andrew S. Tannenbaum, Prentice-Hall, Inc. Andrew Tannenbaum is a must-read for any kernel aficionado, too. This book takes a very academic approach to many of kernel theory's problems, such as dead locks, scheduling, etc.