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Stat textbook recommendations?

I like:

Applied Linear Statistical Models by Neter, Kutner, Nachtsheim, and Wasserman (McGraw Hill)

It is not specific to any stats package, but it gives a good mix of theory behind the routines and how to apply them and covers a good breadth of material.

A must have for statistics and R is:

Modern Applied Statistics with S by Venables and Ripley (Springer).  This gives specific examples and commands to use in S-plus/R along with more background information and theory than the R tutorials.

Once you have the theory down, a couple more books that help with the practical aspects of using R to do the analysis are:

A Handbook of Statistical Analyses Using R by Everitt and Hothorn (Chapman & Hall/CRC)
An R and S-PLUS Companion to Applied Regression by Fox (Sage)

There may be other good ones out there that I am not familiar enough with to recommend.

Hope this helps,