Chambers and Hastie T., Statistical Models with S,
Wadsworth and Brooks.
Ripley B. and Venables W., Modern Applied Statistics with Splus, Springer and Verlag. http://www.stats.ox.ac.uk/~ripley/MASS/
Spector Ph.,An Introduction to S and Splus, Duxbury Press, California.
Here is some online documentation sites:
The very long postscript files that were written before the Springer book of Venables and Ripleys are available at : http://www.math.montana.edu/stat/tutorials/Splus.html
A short handout that explains clearly how to start using Splus: http://www.ms.washington.edu/help/software/splus.html
Charles Van Loan,Introduction to Scientific Computing,
Prentice and Hall.
The matlab is available at the local site by ftp to ftp.cs.cornell.edu in the directory pub/cv.
Sites with Matlab tutorials:
Bootstrap signal processing toolbox for MATLAB: http://www.atri.curtin.edu.au/csp/downloads/bootstrap_toolbox.html
General statistical Ecology matlab functions: http://www.biol.ttu.edu/Faculty/FacPages/Strauss/Matlab/matlab.htm