Where can I find a DC hydro electric generation system for use on my
sailboat (which will be powered by an electric motor when there is no
wind) ?  36 volts or 12 volts capable of being upped to 36.

I once worked on a large steal hulled ketch that allowed you to manual
adjust the feather on the prop.  You could be sailing and feather out
the prop and it would turn a shaft driven alternator.  I don't know if
this solution will be pratical on a boat small enough to be driven by
a dc motor.

I also read that with certain props, if you kill the engine while in
reverse the prop will be stuck unfeathered.
http://www.pyiinc.com/images/pdf/Max-Prop%20VP%20Instructions.pdf

Here are some details on how to chose the correct alternator.
http://www.practical-sailor.com/newspics/charts/85Questions11.pdf

I am still a bit fuzzy on how the transmission will work on this boat.
 It seems stupid to have the motor turning the alternator.  How big is
the boat, and can you give any details on how the motor works?

Hope this is of assistance

what you are looking for is the electric wheel concept, it is used in
regenerative braking on the hybrid toyotas and hondas.  A company that
is currently developing this process for sailboats is solomon,
www.solomontechnologies.com. also another company in england builds
the lynch motor, which can be used the same way if you want to design
a system yourself.

A comment on the solomon technologies comment.  While in a previous
career, at NASA Goddard Space Flight Center, I personally debunked the
claims of that company.  Their Electric Wheel concept is bogus.  If
you look carefully at their propaganda, they are not actually using
that concept, but rather just selling motors with hype.

Simply put, you do not get torque multiplication by running two motors
in opposite directions on the Sun and Ring gears of a planetary.

Also, the Prius uses a similar, but decidedly different concept.  In
the Prius, a motor is directly attached to the Ring gear as is the
output to the wheels.  The Sun is attached to the engine, and the
Planets are attached to a starter generator.  The purpose of that
arrangement is to do several things:

Allow a CVT effect on the engine, by providing a variable reduction
from Sun to Ring by controlling the speed of the Planets.

Allow direct drive of the wheels by electric motor alone with minimal losses.

Allow the starter generator to start the engine independent of car movement.

Allow for engine power to be split between the output to the wheels
via the Ring and as electricity via the planets and starter generator.
 Interestingly, this means that at full power, the engine provides
power through both mechanical means directly and through a rather
circuitous path of engine > starter generator > electric motor.  The
point of doing that is that it allows the engine to provide full power
from a rather low speed on up with no shifting.