Hmm - my reaction is that I'd want to make sure that fuel tanks (and water tanks) are higher (less exposed) than anything else under the vehicle. You can ding a chassis member and not do much damage, however if you crack a fuel or water tank you may be in big trouble. So I'd avoid having either of these as the lowest/most exposed part of the vehicle. I guess you could damage the tool box and it's not so serious.
In terms of minimum clearance, as others note, whatever it is you'll find the limits with experience. I continue to be impressed by seeing Toyota Corollas and similar cars on rough tracks around the world.
Our Montero (at home) has 28.5 cm clearance and our Wrangler (in Canada) has 21.1 cm. My Peugeot 404 Estate had a clearance of 15.2 cm and took me through the Kalahari with no problems - the only modification I had was a water tank below the boot/trunk, and I made sure that it was well within the exterior dimensions of the body.
You also need to consider, as others imply, Breakover, Approach, and Departure Angles.