Thomas, David et al. Agile Web Development with Rails. Raleigh and Dallas: Pragmatic. 2005.
The weblog of Sam Stephenson the creator of RJS and the Prototype library.
Justin Palmer's weblog featuring many in-depth articles about Prototype.
The first reference on the Prototype library. Very in-depth reference, but only covers up to Prototype version 1.4.0.
A wonderful graphical overview of the Prototype library by Jonathan Snook.
Scriptaculous developer Thomas Fuchs' weblog. Chock-full of wonderful effects examples with source code.
An excellent and in-depth article by Abdur-Rahman Advany that explains in detail how to use Scriptaculous effects queues and how the effects queues are used from within Rails.
Rails core developer Rick Olson's site for Rails troubleshooting and tips. Contains a few great articles about RJS.
Kevin Clark's brand new (at the time of writing) plugin that allows you to functional test your RJS templates.