The basic reference is The New S Language: A Programming Environment for Data Analysis and Graphics by Richard A. Becker, John M. Chambers and Allan R. Wilks. The new features of the August 1991 release of S are covered in Statistical Models in S Edited by John M. Chambers and Trevor J. Hastie. In addition there are specifically S-PLUS reference books: S-PLUS User's Manual (Volumes 1 & 2) and S-PLUS Reference Manual (in two volumes, A-K and L-Z).
It is not the intention of these notes to replace these manuals. Rather these notes are intended as a brief introduction to the S-PLUS programming language and a minor amplification of some important points. Ultimately the user of S-PLUS will need to consult this reference manual, probably frequently.