I use Netbeans, it does not get a lot of press but they have been outpacing many of the dedicated JavaScript IDE's they have great JavaScript support.
how do you rename a method for example with the tool use (imagine that another method with the same name exists in a different class/module)
I use Dojo for large JavaScript projects, there really is not an alternative when you get the the application sizes I deal in, as such everything is namespaced. Netbeans can refactor methods in JavaScript, so I use the built in functionality of the IDE to do so.