I purchased a rack system by Rhode Gear this year for my Ironman Canada trip with the trailer.
It is a fork down plate that sits on the floor of the trailer with anti skid rubber on the bottom. It held my road bike and nic's mountain bike perfectly still from Calgary to Penticton BC and back. I placed the rear tires on the rubber door mat and looseley tied them together with a cord. The only concern would be an exceptionally muddy bike, but I think a towel underneath would take care of that.
For 40 bucks, it was a great deal.