All things Java will appear in this book, over time....

It is important to note that the NPAPI is being phased out and so Java Applets will cease to work. See NPAPI Plugin Perspectives and the Oracle JRE (Java Platform Group, Product Management blog) for more details.

The future is in Java Web Start, where a Java app is launched, see Java Web Start in or out of the browser (Java Platform Group, Product Management blog) which provides a good starting point for learning about Java Network Launching Protocol (JNLP).

If you need source code for an Open Source library then CodeNav is a very handy site.

There is Java Enterprise Edition on GitHub, see Java EE.