By default Rails 3 comes with Prototype. But more and more people are switching to jQuery. The project Rails-3-jQuery on Github simplifies the process of switching out the Prototype support to jQuery. It includes jRails that provides drop-in replacements for Prototype and Scriptaculous helper methods to make it a seamless transition.
To update a project, just issue the following command in the project root
rake rails:template LOCATION=http://github.com/lleger/Rails-3-jQuery/raw/master/jquery.rb
For more information on the project, check the project page on Github.