My project was an Atlassian JIRA plugin: Java, SQL, some Velocity templates in the back-end and few dashboard gadgets (JavaScript/HTML/CSS) in the frond-end. Atlassian also have their own frameworks for the plugins, so it is helpful if an IDE has support for nonstandard external libraries.
I've had quite unpleasant experience with Eclipse's JavaScript support, it has numerous glitches with completion and automatic code formatting, especially with complex code (modular sources, few frameworks used, etc.). Refactoring is not always works as intended (or at all) and almost useless. I've not tried Aptana Studio though.
NetBeans is somewhat better in this regard but its support for complex mixed source projects (like Java/JavaScript/web/templates etc.) is lacking (maybe I've not tried hard enough).
Finally I've ended up using IntelliJ IDEA. It is commercial (there is 30 day trial) but unbeatable feature-wise. Code analysis, semantic coloring, refactoring which works across various source files (like js, css, html). Just try it and you would never look back.
P.S. I'm not affiliated with JetBrains in any way, it's just my personal view.