Official R Citation

Ihaka, R. & Gentleman, R. (1996), "R: A Language for Data Analysis and Graphics", Journal of Computational and Graphical Statistics, 5, 299-314. (official R citation for publications that reference R).

Web References

Comprehensive R Archive Network (CRAN). Nearest Site.
Ross Ihaka, R: Past and Future History.
Ian McLeod's R page
R Core Team, Introduction to R. (pdf format)  or  (UWO site)
R Core Team, Writing R Extension. (pdf format).
R FAQ Files:  General, MS Windows, Ian McLeod's
R Online Tutorial

Helpful Fundamental S Books

Becker, R., Chambers, J.M. (1984), S An Interactive Environment for Data Analysis and Graphics, Pacific Grove: Woodsworth.
Becker, R., Chambers, J.M. and Wilks, A.R. (1988), The New S Language, Pacific Grove: Woodsworth & Brooks/Cole.
Chambers, J.M. and Hastie, T.J. (1992), Statistical Models in S, Pacific Grove: Woodsworth & Brooks/Cole.
Chambers, J.M. (1999), Programming with Data: A Guide to the S Language, Springer-Verlag.

Journal Articles on R

Gentleman, R. & Ihaka, R. (2000, to appear), "Lexical Scope and Statistical Computing".
Ihaka, R. & Gentleman, R. (1996), "R: A Language for Data Analysis and Graphics", Journal of Computational and Graphical Statistics, 5, 299-314. (official R citation for publications that reference R).
Murrell, Paul and Ross Ihaka (2000, to appear), "An Approach to Providing Mathematical Annotation in Plots" , Journal of Computational and Graphical Statistics.

Also of Interest to R Users

Clive Loader (1999), Local Regression and Likelihood.  Springer Verlag; ISBN: 0387987754 
Swayne, Deborah F., Dianne Cook and Andreas Buja (1998), "XGobi: Interactive Dynamic Data Visualization in the X Window System", Journal of Computational and Graphical Statistics 7, 113–130 . Homepage.
Venables, W. N.  and Ripley, B.D. (1999), Modern Applied Statistics with S-PLUS. Third Edition. Springer-Verlag. Homepage