R for biodiversity research

Use R - Book series - These books are available online for free if your library is a subscriber. Titles include “Forest Analytics with R”, “Functional Data Analysis with R and MATLAB”, “A Primer of Ecology with R”, “Applied Spatial Data Analysis with R”, etc.
R cookbook - O'reilly series - This book contains over 200 “recipes” (short practical examples). Great book to get started.
Numerical Ecology with R - This new book by Borcard et al. from Université de Montréal discuss both some theory on quantitative methods in ecology and how they are implemented in the R language.
Tree diversity analysis - A free manual and software for common statistical methods for ecological and biodiversity studies.
Ecological Models and Data in R - This is a great book by Benjamin Bolker that covers multiple areas of ecological modeling, mostly in the bayesian framework. The associated wiki can be found here.
Extending the Linear Model with R: Generalized Linear, Mixed Effects and Nonparametric Regression Models
Mixed Effects Models and Extensions in Ecology with R by Zuur et al.

Official R project homepage
R seek a great search engine for R.
Stackoverflow provides users the ability to ask and answer questions related to R. Questions that are well articulated are generally answered promptly. Make sure you search the archives of questions to determine whether your question was asked previously, prior to posting a new question.
R mailing lists You have a problem? Chances are that somebody else had the same problem before you. The archives of the mailing lists provide a wealth of information. They can be searched here.
R for Matlab users For those already familiar with the Matlab language.
R programming for those coming from other languages

R studio - A great new interface/IDE for R that works on Windows, Mac and Linux.
R commander - A cross-platform solution, it also provides an interface with drop-down menus to perform common analyses in a user-friendly way.
Tinn-R - A good, but Windows only graphical user interface for R.
Rkward - This is a nice, clean interface for R. It works on Linux and Windows but the Windows version has some known issues.

ggplot2 - A very elaborate and powerful graphics package based on the system described in “A Grammar of Graphics” by Leland Wilkinson.
Lattice - Another powerful graphics package that allows for many types of plots with sophisticated layouts.

ADE4 - Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences.
primer - A support package for Stevens 'A Primer of Ecology with R, Springer'. Provides functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices.

vegan - Very extensive R package for community ecology
BiodiversityR - Graphical user interface for biodiversity and community ecology analysis.
vegetarian - Jost Diversity Measures for Community Data.
FD - Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology.
untb - A collection of utilities for biodiversity data. Includes the simulation of ecological drift under Hubbell's Unified Neutral Theory of Biodiversity.

ads - Spatial point patterns analysis.
raster - Geographic analysis and modeling with raster data.
gdistance - : distances and routes on geographical grids.
GeoXp - Interactive exploratory spatial data analysis.
spatial - Functions for Kriging (geostatistical method of interpolation) and Point Pattern Analysis.
spatstat - Spatial Point Pattern analysis, model-fitting, simulation, tests.
spatgraphs - Graphs for spatial point patterns.
MarkedPointProcess - Analysis of marks of marked point processes.
spatgraphs - Spatial Point Pattern analysis, model-fitting, simulation, tests.
geodist - Calculates a geographic distance matrix from a table of latitude and longitude information using the law of cosines. Written by Simon Joly.

labdsv - Ordination and Multivariate Analysis for Ecology.
cluster - Cluster analysis extended.
amap - Another Multidimensional Analysis Package, tools for Clustering and Principal Component Analysis.

adegenet - Classes and methods for the multivariate analysis of genetic markers.
adephylo - Exploratory analyses for the phylogenetic comparative method.
hierfstat - Exploratory analyses for the phylogenetic comparative method. - hierarchical F-statistics from genetic data (e.g. Fst value)
ape - Reading, writing, plotting, and manipulating phylogenetic trees. Analyses of comparative data in a phylogenetic framework in general.
edgeR - A Bioconductor package for differential expression analysis of digital gene expression data.
DESeq - Another Bioconductor package for differential expression analysis of digital gene expression data, based on the negative binomial distribution.
DEGseq - Yet another Bioconductor package to identify differentially expressed genes from RNA-seq data.

Books on R