In case you haven't seen it, there are some interesting ideas in the new skin developed by the Blender community for its wiki:
http://wiki.blender.org/index.php/Meta:Skins/Naiad
It was clearly designed especially to support structured documentation:
http://wiki.blender.org/index.php/Doc:2.5/Manual
Among the more interesting ideas employed here are automatic changes to the layout to make the best use of the available screen resolution.
Cheers, Erik