Yehuda Katz has a nice article on the prototype system that I generally point people to.

http://yehudakatz.com/2011/08/12/understanding-prototypes-in...

And the JavaScript Patterns book is a good read to get an overview of what can be done with just JavaScript. If your application is even remotely complex you'll probably end up using something like backbone or sproutcore which provide constructs for organizing your code anyway.