NetBeans and Eclipse are the two most widely used Java IDEs, which also support other languages and formats such as HTML, JavaScript, XML, CSS,
JSP,
JSF, PHP, Ruby, Python, and lots of other stuff.
I'm currently using Eclipse 3.4 at work for a big Java and JavaScript / HTML application. It works OK, but the support for JavaScript could be better. I've also tried NetBeans 6.5, and in my experience its support for JavaScript is better than that of Eclipse. NetBeans also has especially good support for Ruby and other languages.
You'd really have to try them out yourself to find out which one best suits you.