Another good book by John Chambers: "Programming with Data: A Guide to the S Language". As the name suggests it is actually about S, not R, but it provides a lot of valuable information about S4 classes anyway.
There's also some information in the R manuals "Writing R Extensions" and "R Internals" (particularly the latter). Those can be found at http://cran.r-project.org/doc/manuals/.
Finally, I would recommend "How S4 Methods Work", which is a great overview of how to think about S4 as it fits into R.
