I have seen a few quads trailered by standing up on rear wheels. Is this harmful to the quads?

 

Nope. The manufacturers actually have it in the users manual as one of two options for transporting. The wheels down is the preferred method of course.....

 

The owners manual for my '03 Kawasaki Prairie 360 says don't transport it standing on it's tail. Service manager at the dealership said not to stand it up for more than a "short time" for cleaning, inspection and such as oil can migrate into the air box.