This is going to be a fairly common post topic, as a lot of people manage to forget a lot of different muscles that are very specific to trail running, hiking, skiing, whatever, but are often completely overlooked.
I'll be focusing in on a couple of overlooked muscles or muscle groups that are fairly specific to trail running. Runners are notorious for having awesome quadriceps (thigh muscles), sculpted calves, and that's about all. In other words, most runners aren't well balanced. This is often not the case with trail runners, who typically have a more diverse hobby set. This typically means that they're upper body and core muscles are better off, yet I fully believe that most runners, even trail runners don't really do any work for the following muscles.
1. The neck. Tell me, when's the last time you did any neck exercises against resistance? I haven't for 6 years, since college football. Exercises can be found HERE. I personally am a big fan of applied resistance, but rather using a towel (grab it with both hands, one in either corner) to apply resistance. Runners, I'm looking toward the back of the neck muscles. We spend a lot of time looking down, not up. That means our neck muscles up in the front are great... but the ones in back... nottttt so good. Try the exercises, you should start to notice less cramping in the neck after a month or so.
2. Do you even know what the hamstrings are? Sure you use them a lot when you go downhill, but when's the last time you got intimate with them? When's the last time you made them scream with workout burn? Also, can you even touch your toes?
The hamstrings are the muscles in the back of the thigh, just below the butt. If you want the names, insertions, origins, innervations, arterial supply, action, and contribution to gait, I can tell you more than you wanted to know. You don't want to know these things. You want to know how to not get hurt when running.
Try this. Lay down on the ground, with a bench or chair 2 or 3 feet in front of you. Put your legs up on the chair. Raise your butt off the ground, hold for a few seconds, slowly lower the butt back down to the ground. Now try it with one leg. Cry moderately. Repeat.
Another great way to save the hams? Dribble a soccer ball around. A lot of weird positions, a lot of strange kicking. It works.
The hamstrings are going to keep you safe as you go downhill. The neck keeps your head attached to the body. These are both good things. Don't forget to work on them.