I was looking over Underscore.js library and found a link on annotated source code[0]. Do you know such type of annotated source code which you recommended to read?
[0].http://underscorejs.org/docs/underscore.html
Some more links:
Backbone.js - http://backbonejs.org/docs/backbone.html
jQuery 1.6 - http://robflaherty.github.io/jquery-annotated-source/
http://gitlet.maryrosecook.com/docs/gitlet.html
Small Lisp interpreter in Python:
http://khamidou.com/compilers/lisp.py/
If you are interested in annotation formats other than side-by-side, many Jupyter or IPython notebooks would qualify, for example Peter Norvig's programming exercises:
https://github.com/norvig/pytudes