I have a '03 Honda Rancher and was wondering what would happen to the fuel, oil, and other liquids if I put it up on it's tail end for traveling?  

you could get drainback which means you could get an excess of oil in the cylinder head, or lack thereof.

it's normally not a good idea to stand it on end and trailer it.

also the clutches could damaged.  they are covered in oil and if the oil drains off the clutches it could cause premature failure.