John Kruschke also has a website for the book that has all the examples in the book in BUGS and JAGS. His blog on Bayesian statistics also links in with the book.
I personally thought that Modern Applied Statistics with S-Plus ticks all of the boxes you have outlined. Every example has R code, they give good references to other sources, and Venables and Ripley have a wonderfully terse and explanatory writing style which I really appreciated. I tend to re-read the book every so often, and each time I get more from it. Of course, your mileage may vary.
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John Kruschke released a book in mid 2011 called Doing Bayesian Data Analysis: A Tutorial with R and BUGS. (A second edition was released in Nov 2014: Doing Bayesian Data Analysis, Second Edition: A Tutorial with R, JAGS, and Stan.) It is truly introductory. If you want to walk from frequentist stats into Bayes though, especially with multilevel modelling, I recommend Gelman and Hill.
John Kruschke also has a website for the book that has all the examples in the book in BUGS and JAGS. His blog on Bayesian statistics also links in with the book.