Scriptaculous and Prototype are, by the way, included in the Rails distribution itself so no need to explicitly integrate them...
As the previous poster pointed out, Prototype and Script.aculo.us are distributed as part of Rails. In addition, Rails itself has helpers to make them easier to integrate. If you wanted to create a hyperlink which, when clicked, executes an Ajax call instead of redirecting the user, you can simply do this in your view:
There are Rails helpers for most of the Prototype and Script.aculo.us features.
subject: Integrating Rails with client side technologies