Zen

• 
  Synchronicity and the Stories of Our Lives by Robert H. Hopcke
  The book discusses synchronistic events without any mumbo-jumbo.

  Hopcke's web site

• 
  A Gradual Awakening by Stephen Levine
  A gentle introduction to meditation, starting by focusing on one's breath. Why breath? Because it is always with us!

• 
  Finite and Infinite Games by James P. Carse
  One of the best books I have ever read.

• 
  If the Buddha Dated : A Handbook for Finding Love on a Spiritual Path by Charlotte Sophia Kasl, Phd.
  Much more than for dating ... From this I learned that namaste means: 'I honor that of god in you' or 'I bow to the light in you' (page 205-206).

Science

• 

  The Planiverse: Computer Contact With a Two-Dimensional World by A. K. Dewdney
  A lovely variation of Edwin Abbott's classical Flatland.

  
  
  

• The Search for Solutions by Horace Freeland Judson
  The book is a wonderful exposition of how science really works. Unfortunately this book is out of print, but Amazon may be able to get you a copy.
  However, it seems to be available from The Association of American University Presses.

• Maxwell's demon: why warmth disperses and time passes by Hans Christian von Baeyer
  This is an excellent introduction to thermodynamics. It is not technical but has many insightful examples, such as describing the entropy as the number of digits of the number of ways a system can be arranged. There are few technical errors. However towards the end Landauer and Bennett are given credit for solving the demon problem, whereas they have truely muddied the waters.

• 

  The New Way Things Work by David Macaulay. If this is anything like the original The Way Things Work, then it is spectacular!

  
  
  

Science and Religion

• 
  Skeptics and True Believers : The Exhilarating Connection Between Science and Religion by Chet Raymo
  

• 
  Phantoms in the Brain by V. S. Ramachandran and Sandra Blakeslee
  This is a spectacular book. Ramachandran and Blakeslee use examples of strokes in different parts of the brain to begin to dissect how the brain works. Highly recommended.

• Classics of Free Thought by Paul Blanshard. A spectacular tour of powerful arguments against religious idiocy.

On Writing Well: The Classic Guide to Writing Nonfiction by William Knowlton Zinsser. This inspired a little ditty. It helped me a lot when I wrote molecular machine theory papers Level I and Level 2.