For me, it greatly depends on the trailer and the horse. For my older horses that have been hauled a few million miles, I am completely comfortable throwing them in the trailer loose. They know what hauling is all about and they get into a position that is comfortable for them and they ride that way. If the horse is young (like a colt) or if I am hauling horses that are unfamiliar with each other, I will usually tie them just to make sure that they don't get to making circles around the inside of the trailer.
Some horses are better off loose, others are better off tied, and sometimes what they prefer depends on which horses they are riding with and the type of trailer they are riding in. I, personally, prefer to tie them first until I know them well enough to know how they are going to ride. After that, I can adjust how I haul them to fit.
Oh, and I haul my horses in stock trailers.