Joomla 1.6.0 includes Mootools Core 1.3 and Mootools More 220.127.116.11 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:
Many old functions have been removed or renamed in Mootools 1.3. Thanks to the compatibility module they still work fine in Joomla 1.6, however a future version of Joomla is likely to remove the compatibility module. It is recommended to follow the Mootools' Upgrade from 1.2 to 1.3 guide to future proof your code.
Also new in Mootools 1.3 id, 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.