Comment by bretthopper

Looks great. I think you could further improve navigation by adding a section menu for each page like Bootstrap docs do (on the left): http://twitter.github.com/bootstrap/getting-started.html

For example, on http://jqfundamentals.com/chapter/traversing-manipulating, you could have the top level headers in a sidebar nav that uses the affix plugin. You can get a bit lost since the pages are quite long. This would help quickly see all the sections and jump between them.