VSDoc is an awesome way of commenting Javascript, and I particularly like the ability to make one Javascript file 'depend' on another. This paves the way for Javascript minifiers/combiners that take into account proper ordering of script includes.
The only thing that might bother some is that it's VS-Doc.
Are there any competing formats that are vendor-neutral?
And how widely is the VSDoc standard used by non-Microsoft IDEs such as Eclipse, etc?
The standard that is used the most is JsDoc, as implemented by jsdoc-toolkit. The syntax is short and concise, and is easy to parse.
There are many tools that can generate documentation from these, such as ext-doc, and most IDE's have built in support for this.
This does not have any statements for annotating dependencies, but this is really more a minifier issue than a documentation issue as any comment can include the list of dependencies.