The Green Tea Press books are great; and free.

Think Python: How To Think Like a Computer Scientist http://www.greenteapress.com/thinkpython/thinkpython.html

Think Complexity: Exploring Complexity Science with Python : http://www.greenteapress.com/compmod/

Think Stats: Probability and Statistics for Programmers : http://www.greenteapress.com/thinkstats/index.html