There are two parts to the "dojo jsdoc" process. There is a parser, written in PHP, which generates xml and/or json of the entirety of listed namespaces (defined in util/docscripts/modules, so you can add your own namespaces. There are basic usage instructions atop the file "generate.php") and a Drupal part called "jsdoc" which installs as a drupal module/plugin/whatever.
The Drupal aspect of it is just Dojo's basic view of this data. A well-crafted XSLT or something to iterate over the json and produce html would work just the same, though neither of these are provided by default (would love a contribution!). I shy away from the Drupal bit myself, though it has been running on api.dojotoolkit.org for some time now.
The doc parser is exposed so that you may use its inspection capabilities to write your own custom output as well. I use it to generate the Komodo .cix code completion in a [rather sloppy] PHP file util/docscripts/makeCix.php, which dumps information as found into an XML doc crafted to match the spec there. This could be modified to generate any kind of output you chose with a little finagling.
The doc syntax is all defined on the style guideline page:
http://dojotoolkit.org/developer/styleGuide#Documentation