JSAnalyse has just been published on codeplex. It is a tool which analyses the dependencies between javascript files. You can even define the allowed dependencies and JSAnalysis checks whether the defined rules are fulfilled or not. That allows to keep track about the javascript dependencies even in big projects and to have a clean architecture.
JSAnalyse can be executed as a command line tool or configured via the Visual Studio Layer Diagramm. It is also easy to integrate into the build. With gated check-ins you can keep the dependencies under control.