A Handbook of Statistical Analyses Using R, Second Edition by Hothorn, Torsten, Everitt, Brian S. [Chapman and Hall/CRC, 2009] (Paperback) 2nd Edition [Paperback]
This is not your standard statistics book nor your standard book on R. It is best for people who already know something about each. Each chapter is devoted to different statistical topics, but in each the author analyzes a different data set showing each step as it would be implemented using R.