It depends -- personally, I've found Underscore.js' code to be very enlightening for how to structure simple toolkits. They just added an annotated version as well.
Knockout is also quite interesting, and presents a few techniques that you might not see in a more normal library like jQuery or Mootools.
Not that the code for jQuery or Mootools (or Dojo or YUI or ... you get the idea) is bad -- quite the opposite! There is an amazing amount to be learned from these libraries, and I cannot recommend enough looking up the declaration of a method that you find intriguing in any of these libraries and following the breadcrumb trail -- it's a real learning experience!
So dig in ... there's lots to see, and very little time to see it!