Thanks for the feedback John and dharlow. It has been a while. I checked my previous posts and it's been about 6 months since I last logged in and about 12 months since I posted regularly. I can't think of any specific reason why I stopped logging in here though.
Anyway, this is the book I'm referring to:
http://www.amazon.com/JavaScript-Definitive-Guide-David-Flanagan/dp/0596805527/
On the O'Reilly site its $39 or something and the kindle version is $27 so I bought that version. Then on the last page of the kindle version there's a link which you can use to "upgrade" to the multi format digital version from O'Reilly, so I did that as well. This means I have the Kindle version, and ePub version, a PDF version and a mobi version (which is the kindle format).
The ToC in the different versions is properly linked as you would expect, it's just not the best experience trying to find a specific topic quickly. It definitely needs rethinking, on an iPhone anyway.