From Moodle 2.9 onwards Moodle will start using the Asynchronous Module Definition(AMD) API for writing JavaScript modules.
AMD API is a standard API for creating Javascript modules and you will find many useful third party libraries that are already using this format.
Before Moodle 2.9 YUI was used to write Javascript in Moodle but As of Moodle 2.9, it is decide start transitioning to jQuery and Javascript Modules because Yahoo has ceased all new development on YUI
There is a small how to guide for developing JavaScript modules for Moodle here.
For more details about using JavaScript and jQuery please check out these Moodle docs:

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