Hey, I'm the author of the CoffeeScript 
book<http://pragprog.com/book/tbcoffee/coffeescript> from 
PragProg. I noticed this conversation and thought I'd stop by.

CoffeeScript goes great with either Prototype or jQuery. (One chapter of my 
book is a primer on jQuery.) As Walter said, while it's possible to use both 
Prototype and jQuery on the same web page, it's generally not very efficient 
because both libraries offer much of the same functionality. Prototype has 
traditionally had a large following among Rubyists because it provides lots 
of Ruby-like idioms. But jQuery is much more widely used and actively 
updated than Prototype, and is the official JS library as of Rails 3.1—even 
though the creator of Prototype, Sam Stephenson, works for 37signals. (He's 
also become a strong advocate of CoffeeScript and was a technical reviewer 
for the book.)

So, in short, I'd suggest sticking with CoffeeScript + jQuery. If you miss 
Rails' functional programming goodness, check out 
Underscore.js<http://documentcloud.github.com/underscore/>. 
And if you feel like modifying native prototypes (e.g. adding an 
uppercasemethod to all strings), feel free. Check out how Prototype does 
it: https://github.com/sstephenson/prototype/tree/master/src/prototype/lang

If you have any questions, you can always find me on Stack Overflow.

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