The trailer places install a dense closed foam on the trailer floors.  It's nice, but has to be replaced where they paw, etc.  I can't remember what it cost per stall, but it wasn't crazy high.

A few members in our club use multiple layers of standard mats. It's inexpensive and quite "cushy". Overlap the edges so they don't align.

Gard

There is a product that our dealership sells that is a closed cell polymer that doesn't take on moisture.  It goes between your floor and the floor mats.  It is very light weight and is easy to install.  All that is needed is a straight edge, utility knife and tape measure.  It comes in a roll and measures 50+ inches.  I personally use it in my own trailers (I'm a trailer salesman).  It definitely reduces leg fatigue and soreness.  It is the difference of you wearing a thin leather soled boot/shoe and a gel-soled Nike tennis shoe.  It runs about $8.25 - $8.50 per running foot.  If you use your trailer a lot, it will need to be changed annually.  In time it gets compressed, and loses its cushioning effect.  Customers that compete in performance events call it there "secret weapon"; as there horses come off the trailer a lot fresher.  I call it "poor man's air-ride".  Once you try it, you will use it regularly.