What functionality is available from Drupal.theme()
These are the JS theme functions defined by core:

Tabledrag


Drupal.theme.prototype.tableDragChangedMarker
Drupal.theme.prototype.tableDragIndentation
Drupal.theme.prototype.tableDragChangedWarning


Vertical Tabs


Drupal.theme.prototype.verticalTab


Overlay Module


Drupal.theme.prototype.overlayContainer
Drupal.theme.prototype.overlayElement


Many contrib modules also define their own theme functions, it's not possible to list all of those here so your best best is to run a grep -nr "Drupal.theme.prototype" /path/to/drupal and see what's available in your own installation.

It's also worth bearing in mind that individual theme functions will only be available in the page if the file that contains them has been included. So if the Overlay module is disabled, for example, the related theme functions won't be available. If the vertical tabs JS hasn't been added that won't be available, and so on.