I use the prototype.js javascript framework daily and as a result having an update-to-date API reference is essential. Thankfully, you can view the entire API online at the prototype.js website in an easily accessible form.

Personally I find PDFs a bit easier to manage for API references.    Josh Clarke at GlobalMoxie has put together a PDF version of the Prototype.js documentation with the blessing of the development team.

Update 25th March 2008: Josh has just updated the PDF to Prototype version 1.6.0.2 which is the latest version of the prototype API.  More information is available here:

http://globalmoxie.com/projects/prototype-pdf/index.shtml