This web site lists some of my personal favorites. I've tried only to list links I find myself using over and over again. Well, first things first.
Lets clear up a common confusion.
JavaScript is not Java. Java and Javascript are different technologies made by different companies for different purposes. JavaScript is a scripting language invented by Netscape to programmatically control web browsers. Java is most famous for applets, servlets, and Java server pages. Applets are small computer programs that get downloaded with a web page.