[villek]

I found the annotated source code of the underscore.js to be very educational: http://underscorejs.org/docs/underscore.html

[joshuacc]

Worth pointing out that the tool used to produce the annotated version is open source, and annotated by running it against its own source code: http://jashkenas.github.io/docco/

[msvalkon]

I have to say that the annotation is very nice. Would be a nice feature for something like Github, assuming that developers care enough to do the write up. Might get messy for larger projects though.