The Sun Developer Network is the most important Java portal on the web:
You should have a link to a local copy of the Java APIs. This is the most frequently referenced document for Java programmers. It documents all of the Java class libraries. An online version of the 6th edition can be found at:
http://java.sun.com/javase/6/docs/api/
The best reference for the Java language itself, apart from the libraries, is Peter Setsoft's book, Java Precisely, 2nd Edition. MIT Press. The formal specification of the language can be found here.
The Java Tutorials are a good slow paced way to teach yourself Java:
http://java.sun.com/docs/books/tutorial/
The Java Style Guide tells you about coding conventions used by Java programmers.
The Javadocs page is a good reference for using the javadoc tool.
The two most popular open-source IDEs are NetBeans and Eclipse.
A good introductory text for Java is Cay Horstmann's Java Concepts for Java 5 and 6, published by Prentice Hall. The book also has a student companion web site.