We've just released our Mobipocket/Kindle output on Feedbooks and we already got TOC support through an inline-HTML TOC at the end of the book (it's referenced as a TOC in the guide).
With Mobigen, you can add a TOC if you use an OPF file instead of a single HTML file.
Try Feedbooks if you're looking for an example:
http://www.feedbooks.com/discover