What's the best book for learning about Java security?

Govind Seshadri

I've found Inside Java 2 Platform Security by Li Gong, the "father" of Java security to be an excellent reference.

For an excellent introduction, try the chapter on Java Security within Core Java by Cay Horstmann and Gary Cornell.

If you are doing any advanced encryption with Java, having a copy Java Cryptography by Jonathan Knudsen should prove useful.