Netbeans has very good JavaScript support and in browser JavaScript debugging. It is the only one I know of so far that does in-browser debugging. VS and IE do but IE's debugger is primitive. Netbeans allows you to debug and trace through the entire stack in one location. I went through a lot of them Aptana, Eclipse, et. al. and found that Netbeans provided the best JavaScript development tools in my opinion.
Where applicable, I use MS Visual Studio - applies "intellisense" to your JavaScript code and supports "step though" code debugging with access to variable values.
JetBrains WebStorm. Basically a stripped down version of IntelliJ IDEA for javascript. Moved to it from Aptana and have never looked back.
VIM as well. Since you're advised to keep everything in one file, handling 5000+ lines of code requires a snappy editor.
Working on a 5000+ line file sucks. It's much better to have multiple files and serve a concatenated + minified version to the browser