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.

The original version of this guide was a great introduction to jQuery for me (thanks!). Overall this looks like a much easier and more interactive way to go through the material.

I do have one comment, though: After reading through the single-page guide, I went back to it for a few weeks and often used Ctrl-F to find specific references to things I couldn't exactly remember how to do, and I don't see a way to search similarly in the new version. Ideally the improved navigation should eliminate the need to use such a blunt tool, but I still wonder if someone might want to come back and find something, remembering some random syntax but not remembering where it was. Not sure exactly how you would fix that in the new guide, or how serious it is, so it's just some food for thought.

Slightly related: Alternative jQuery Documentation http://jqapi.com/

This is the basics guide that the main jQuery site desperately needs on theirs. Great job. Slick implementation of Bootstrap.

What a fantastic site! Sent it round the office web devs!

Awesome, this is much more manageable for my brain.

Just skimming on my iPad...looks very clean with clear navigation. Well done on the welcoming-design side