I use R for data analysis and visualization. Below are some books, websites and articles I have found useful so far. I will add more as I come across other resources.

Books:
An Introduction to R by Venables, Smith, & the R Development Core Team
The R Primer by Claus Thorn Ekstrom                                                                                             Data Analysis Using Regression and Multilevel/Hierarchical Models by Andrew Gelman & Jennifer Hill

Articles:
R Inferno by Patrick Burns

Websites:
ggplot2
R-bloggers
R Home Page
Quick-R
Some Hints for the R Beginner
R Cribsheet by Andreas Buja