Ryan Campbell shows how to get the Prototype library up and running, and introduces and documents Protoype's $() function. Form helper functions, getElementsByClassName functions, Element helper functions, Ajax support, timer functions are all covered.
Michael Mahemoff runs into a problem with Protypes $$ function when looking for class names. Its taking over 90 seconds when more than 100 matches are returned. The advice is: Avoid $$(".classname") on large DOMs.