A start on the User Manual; appearance; other opinions

As there seems to be a discussion of formats ... I would recommend
Texinfo, the standard GNU format.  

I have used this for a 500+ page manual involving a lot of
mathematics, and it works fine in my opinion (see the documentation
links at http://sources.redhat.com/gsl/ for example).  It was also
used for the 'GNU Emacs Calc' and 'GNU R' manuals, which are
mathematical too.

I have successfully converted the file from Texinfo into the following
formats:

   HTML (with and without equation images -- I prefer without), 
   PDF (with scalable fonts), 
   Windows WinHelp (& HTMLHelp)

as well as Postscript (US Letter, A4, and 6"x9" trade paperback) and
Info of course.

I have tried some of the other solutions out there at various times
and they did not match up to Texinfo under heavy usage in my opinion.

regards
Brian Gough