I think the standard usage for non-secure .mobi (.prc) files must be
Code:
mobigen.exe your-source-file.html -c1 -s0
I base this on FBReader failing to read "-c2" files (but working on all non-secure MobiPocket files from the major sites I have tried).
The way to get a TOC into the .mobi file is to give it an .opf file as input, i.e. give it an OEB e-book. I tried this with an OEB e-book "exploded" by ConvertLIT from a MS Reader .lit file, and this worked very well. Unfortunately, even though many e-books formats (including .lit and .mobi) are based on OEB, there are very few native OEB tools available.