Aptana, Eclipse, and Netbeans all support HTML, CSS, JavaScript and Java.
Aptana is actually Eclipse under the covers with what looks like better support for web applications.
I have used Eclipse extensively and found that it was sufficient for my Java web development work.
Recently I have switched to using IntelliJ IDEA after using their JavaScript IDE - Webstorm. IntelliJ IDEA is a full-featured IDE with great support for various languages and frameworks. Webstorm (as far as I can tell) is a cut-down version of IntelliJ IDEA specifically focused on JavaScript development.
The great thing about IntelliJ IDEA and Webstorm is their support for mixed languages. That is, if you have HTML, CSS, and Javascript all in one file, it understands it all and highlights, and formats, the code for you properly. Another great feature are the code inspections which analyse your code for errors and common mistakes - this is a great feature.
Both IntelliJ IDEA and Webstorm are paid applications, but you can try them out for free for 30 days.
I would highly recommend trying out IntelliJ IDEA and/or Webstorm.