I finally figured out how to document a jQuery UI plugin with jsdoc-toolkit

Here is my code:

http://git.sugarlabs.org/projects/karma/repos/mainline/blobs/master/js/ui.scoreboard.js 

EDIT: fixed URL

and here is the generated documentation

http://karma.sugarlabs.org/docs/index.html

of additional interest, I use a Jake task, Rake in JavaScript to generate the docs

Here is my Jakefile 

http://git.sugarlabs.org/projects/karma/repos/mainline/blobs/master/Jakefile