The North Face Better Than Naked Long Haul $80
Trail runners often wisely opt for a slightly longer short. The Better Than Naked Long Haul does an excellent job protecting your thighs from branches and thorns while on the fly through tight singletrack.
This short (and others by the North Face) have nice details for trail runners, such as a tuckeable outer drawstring and plenty of stow pockets. The built-in underwear are also indeed better than being naked out on the trails.