I totally agree about the downhill being hardest on the muscles. I was looking on the internet and it seems a general consenus on most websites that in order to mimic the downhill motion you need to really focus on the negative part of a leg exercise. Below is one of the sites and it suggests to perform slow lowering movements for leg exercises. Hope this helps!
This is copied and pasted from the following link
http://www.healthy.net/scr/column.asp?ColumnId=12&ID=401
Hiking Application
While strength training is clearly advantageous for rock climbing activity, its benefits for hiking performance may be less obvious. Generally speaking, hikers should have a strong and balanced muscular system for all kinds of ambulatory actions up and down trails and mountainsides. The basic strength training program is therefore similar to that for rock climbing, and should include exercises for the quadriceps, hamstrings, hip adductors, hip abductors, pectoralis major, latissimus dorsi, deltoids, biceps, triceps, low back, abdominals and neck muscles. With this on mind, both the single-joint strength exercise program presented in Table 1 and the multiple-joint strength exercise program presented in Table 2 are highly appropriate for hikers.
Due to the nature of most hiking outings, strength training technique is extremely important. For example, hiking up the mountain is hard work that places considerable stress on the thigh muscles. However, hiking down the mountain is also hard work that places even more stress on the thigh muscles. This is because downhill hiking emphasizes negative muscle contractions that attenuate the force of gravity and prevent you from tumbling head over heels down the mountain. Negative muscle contractions cause much more microtrauma to the tissues and often lead to muscle soreness the day following the activity.
With this understanding, it would appear useful for hikers to emphasize negative muscle contractions in their strength training programs. We are not in favor of performing negative only exercise routines with heavier than normal weightloads, because excessive muscle overload can cause serious tissue damage. However, we do recommend performing slow lowering movements to accentuate the negative phase of every repetition. For example, if you take two full seconds to lift the weightload and four full seconds to lower the weightload, the negative muscle contraction receives ample attention. This should enhance the overall training effect, and translate into better muscle response to both uphill and downhill hiking.
Because hikers frequently carry packs on their backs, it is important to develop strong upper body muscles as well as strong leg muscles. The recommended training program should be sufficient in this regard, as long as you train with reasonable intensity. One set of each exercise is highly effective if you use enough resistance to fatigue the target muscle group within eight to 12 controlled repetitions. Two or three 30-minute training sessions per week should produce excellent strength gains, and this represents an important investment for better activity performance as well as improved physical fitness.
