According to this blog post:

http://metajack.wordpress.com/2008/07/01/the-state-of-javascript-documentation-tools/

Natural Docs would be the best choice for that but since the article is almost 2 years old, we might give a second try to those before settling on a particular tool:

JsDoc
HeaderDoc

Interestingly, JsDoc is written in Javascript so we might as well go for Javascript all the way ;-)

To be a little more objective on the choice of tool, we might want to check the following issues:

1. Automatic doc from source code (What style of programming is supported?)
2. What explicit comment tags are supported?
3. What is the quality of the documentation output?

I suggest looking at this next week.

Erick