Joomla 1.6.0 includes Mootools Core 1.3 and Mootools More 188.8.131.52 including all it's modules.
If your extension uses Mootools you can use the following code to include the framework in Joomla's output.
Mootools Core and Mootools More:
The most important difference between Mootools 1.3 and older versions is, that the $() function is deprecated. Instead document.id() should be used.
You can find more information, examples and Mootools plug-ins on the Mootools Homepage.