Table of contents:
 RProject Official Sites
 Tutorials and the Basics in R
 R Packages
 R GUIs and editors
 R, Maps, GIS and spatial data
 Data Integration
 Applied R
 R Blogs
 Data Mining
RProject Official Sites

The R Project for Statistical Computing
Official Site 
Download R Project
Select a mirror and Download R 
The R Manuals
Official R Project Manuals  The R Wiki

The R Journal
The R Journal is the open access, refereed journal of the R project for statistical computing. It features short to medium length articles covering topics that might be of interest to users or developers of R
Tutorials and the Basics in R

An Introduction to R
Notes on R: A Programming Environment for Data Analysis and Graphics 
Using R for Data Analysis and Graphics: Introduction, Code and Commentary
By J H Maindonald, Centre for Mathematics and Its Applications, Australian National University. 
A Brief Guide to R for Beginners in Econometrics
Mahmood Arai Department of Economics, Stockholm University 
R Data Analysis Examples with annotation
Compares approaches with other statistical packages including Stata, SAS, SPSS, Mplus, G*Power and Sample_Power 
Introduction to the R Project for Statistical Computing for use at ITC
Tutorial with useful info on plots 
QuickR Website
R is an elegant and comprehensive statistical and graphical programming language. Unfortunately, it can also have a steep learning curve. I created this website for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R. My goal is to help you quickly access this language in your work.  QuickR: Advanced statistics
 R Tutorials from Universities Around the World
 A tutorial for Lattice
 Multiple tutorials for using ggplot2 and Lattice

Statistics in R
Beginners notes in French and English  Cheat sheet for R  In English
 Cheat sheet for R  In French
 Rtips

Resources to help you learn and use R
From UCLA Academic Technology Services  R Fundamentals and Programming Techniques
 John M. Chambers Publications

University of California (Riverside) R manuals
Simply put, these manuals contain some of the best documentation I have ever seen about how to use R (and Bioconductor).  USING THE R STATISTICAL COMPUTING ENVIRONMENT TO TEACH SOCIAL STATISTICS COURSES

The R Inferno
If you are using R and you think you're in hell, this is a map for you 
Chart of R Colors
Find the right colours for your charts
R Packages
 Crantastic: a community site for R packages where you can search for, review and tag CRAN packages

The Omega Project for Statistical Computing  List of R Packages
Packages listed include: RFirefox, RKML, RGoogleStorage, REuPathDB, WADL, RExcelXML, RGoogleDocs, REuPathDB, WADL, SpiderMonkey, ROpenOffice, GeoIP, RGCCTUFFI, RAutoGenRunTime, Rffi, RGCCTranslationUnit, XMLRPC, RCurl, Google Earth plugin and R, RWordpress, XMLRPC, RKMLDevice, RKML, RHTMLForms, RFreetype, RGoogleTrends, RTidyHTML, RNYTimes, RESTrelated packages, RAmazonDBREST, RDocbook, XMLRPC, RExcelXML, RUbigraph, RKML, R2GoogleMaps, RJavaScript, RAmazonS3, RRuby, Rcrypt, RGraphicsDevice, FlashMXML, XMLSchema, SSOAP, XML, RCurl, Rcompression package, Sxslt package, SJava, Rexif, CGIwithR, Aspell, RDCOMEvents, Combinations, RMatlab, RCurl, Rstem, IDocs, XSL files for Omegahat, SASXML, RDCOMServer, RDCOMClient, RGnomePrint, GccTranslationUnit, SWinTypeLibs, SWinRegistry, S language binding to the gtk+extra library. , S language binding to the Gdk pixbuf library. , S language binding to the Glade library. , A plugin eventloop for R. , S language binding generator for Gtkbased libraries. , R/SPlus XML Parsing package, RGtk package , An RXLisp interface , RObjectTables package , RGtkViewers package, RSMethods, RSPython, RSPerl, RGnumeric, R embedded in Xalan, the XSL translator, R Plugin for Netscape 
Rob J Hyndman  List of R Packages
Packages listed include: FPP, Demography, hts, ftsa, fts, expsmooth, Mcomp, fma, forcast and rainbow. 
plyr  The splitapplycombine strategy for R
plyr is a set of tools for a common set of problems: you need to split up a big data structure into homogeneous pieces, apply a function to each piece and then combine all the results back together. 
The quantmod package
The quantmod package for R is designed to assist the quantitative trader in the development, testing, and deployment of statistically based trading models.  Rattle: A Graphical User Interface for Data Mining using R
 eBook  Data mining with R: Learning with case studies
 Introduction to the Text Mining package in R
 Ggplot R graphics
 Ggplot Vs Lattice
 PMML: An Open Standard for Sharing Models

CGIwithR package
This package allows one to use R scripts as CGI programs for generating dynamic Web content. HTML forms and other mechanisms to submit dynamic requests can be used to provide input to R scripts via the Web to create content that is determined within that R script  XML: Tools for parsing and generating XML within R and SPlus
 RKWard, improved package management, and more

GRaF: Species distribution modelling using latent Gaussian random fields
Functions to fit, visualise and compare Gaussian Random Field species distribution models
R GUIs and editors
 R Commander is a robust GUI for R
 Poor Man GUI for R
 JGR is a Javabased GUI for R
 TinnR makes for a good R editor
 An Eclipse plugin for R
 Instructions to install StatET in Eclipse
 Komodo Edit R editor
 RedR: A open source visual programming GUI interface for R

RM4Es Version 0.2
With the RM4Es version 0.2, you can conduct advanced linear regression, logistic regression and structural equation modelling as easy as doing a few clicks. 
Welcome to RStudio
RStudio is a free and open source integrated development environment (IDE) for R.
R, Maps, GIS and spatial data
 SpatialAnalyst.net
 Thematic Maps with R
 Geographic maps in R
 RGoogleMaps package
 Google Charts with R: Maps

EDENext sample rscripts
Includes info on Shapefiles and Projections in R, and scripts on: Multiple Euclidean Distance Calculator; Decimal Degrees to Degree Minute Seconds (DMS) Converter
Data Integration
 A tool to make R usable from Excel
 Embed R data frames in Excel via multiple approaches
 Connect to MySQL from R using RMySQL package
 Info about pulling data from SAS, STATA, SPSS, etc into R

Sweave is a tool that allows to embed the R code for complete data analyses in latex documents
To create dynamic reports, which can be updated automatically if data or analysis change. Instead of inserting a prefabricated graph or table 
R2HTML project
R2HTML is a package for R, which includes HTML function and methods to output R objects to HTML.
Applied R
 Time Series Analysis and Its Applications: With R Examples: Third Edition
 Has lecture notes with R code A brief guide to R and Economics
 Advanced Topics in Time SeriesEconometrics Using R
 Guide to Credit Scoring using R
 Social Network Analysis using R
 Web Scraping in R
 Revolution Computing: Commercial versions of R
 R Graphical Manual
 The [r] tag on Stack Overflow
 RStatistics component collection for Pipeline Pilot
 Journal of Statistical Software
 For Bioinformatics in R, check out the Bioconductor project
 Social Network Analysis Labs in R and SoNIA
 CRAN Task View: Computational Econometrics
 RSeek: search engine for R functions, lists and more
R Blogs

Rbloggers
R news and tutorials contributed by (320) R bloggers (consolidated blog) 
R you ready
Mark Heckmann's personal R learning blog 
Learning R
Finding my way around R  Romain Francois' R Blog
 One R Tip A Day
 WinVector R Articles
Data Mining
 Data Mining Tools comparison blog post

KNIME (Konstanz Information Miner)
A userfriendly and comprehensive opensource data integration, processing, analysis, and exploration platform.  RapidMiner

Elefant (Efficient Learning, Largescale Inference, and Optimisation Toolkit)
An open source library for machine learning 
Orange
Open source data visualization and analysis for novice and experts. Data mining through visual programming or Python scripting.  Poll on Data mining tools used from KD nuggets
Many thanks to the LinkedIn RProject User Group and specifically Harsh Singhal who provided the original list of links for which we have updated and added to.