Venables WN and Ripley BD (2002). Modern Applied Statistics with S (4th edition). Springer-Verlag, New York. Online material. (Note earlier editions of this book were titled "Modern Applied Statistics with S-Plus.)
Krause A and Olson M (2005). The Basics of S-PLUS (4th edition). Springer-Verlag, New York. Online material. Online version of 3rd edition (Harvard PIN required).
Chambers JM (1998). Programing with Data: A Guide to the S Language. Springer-Verlag, New York. Online material.
Venables WN and Ripley BD (2000). S Programming. Springer-Verlag, New York. Online material.
Becker RA, Chambers JM, & Wilks AR (1988). The New S Language. Wadsworth & Brooks/Cole, Pacific Grove, CA. (Out of print)
Chambers JM and Hastie TJ (1992). Statistical Models in S. Wadsworth & Brooks/Cole, Pacific Grove, CA. (Out of print)