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I just recently started learning RoR and found that Prototype.js is a default javascript library coming from the box. Why does it use this library and why not jQuery, Dojo, Mootools, ExtJS etc.?
It was a choice made about five years ago, and was basically just the favorite JS framework of DHH at the time. Rails 3 will support switching that easier, but for rails 2, you can always just use http://github.com/aaronchi/jrails to swap in jquery for prototype.
UPDATE: As of rails 3.1, it will use jquery by default, and prototype will become available via a gem.