We’ve just finished retiring the YUI tree control that was being used to maintain Taxonomies and replaced it with the jQuery friendly jsTree. This is the first step in migrating the admin interface to use jQuery only (and completely removing Prototype). The new jsTree provides much more precise drag & drop functionality allowing you to re-order and drop nodes under new parents quite easily. The UI has also be tested under FF3 and Safari3 on OSX as well as FF3 and IE7 on Windows and seems to play well on all platforms, please feel free to log any cross-platform issues discovered.
jQuery is currently running using the noconflict option for the Administration interface only, this should help avoid any issues with Prototype during the transition. We plan in enable noconflict() on the customer facing interface at some point in the future to allow developers to use Prototype if they wish in their site extensions.