I agree a lot with what Zach says above. But as there are many different people with as many different types of physical characteristics, there are probably an uncountable number of different training techniques.
I for one, am someone who can hike in the 12-20 mile range (depending on elevation gain) with normal fatigue. At the end of a hike of that distance, I feel exhausted, but I am not totally wasted. I used to feel a lot of pain in my right hip after a long and demanding hike. But joint pain like that, as I am told from doctors and trainers, is something that just needs to be conditioned to meet the demands from long hikes. So by that nature, getting in as many conditioning hikes as possible will soon eliminate the hip pain. But, on the same token, there may be some people, especially older people, who have just "worn out" some of there joints and there isn't much they can do any more to condition those areas.
As far as muscle aches, back aches, pulled tendons, etc, most of these are simply brought on by over exertion, lack of conditioning, lack of warming up, sometimes lack of proper eating and lack of proper amount of fluids in your body. So these can be avoided or reduced by eating enough and drinking enough before a hike. Also, doing various excercises before and between each trip will greatly reduce the soreness in muscles. I am one who will admit I have very poor eating habits and I am also very bad at drinking enough water. So these are my downfalls on many of my hikes and one which I have been focusing on and have noticed a tremendous difference. In fact the difference has been so great that I have experienced no sore muscles in my last 10 hikes or so.
Those that know me, know I have been experiencing great pain in the inside of my hip area, but I know from years of playing college sports, and many other activities, this is not a pulled muscle or injured tendon. I actually have an appointment for an MRI next week.
As far as feet go, yes - 90% of the pain in feet can be eliminated by proper fitting boots and the corrct type of insoles. I used to get sore feet in my mountaineering boots, but the last few trips I've had with them, I've had "Superfeet" insoles and it was like night and day. My feet were so comfortable, I never had to pay a thought to them the entire trip. I now use them in my regular hiking boots and they are nearly as comfortable as wearing plush slippers. Well, maybe not that good, but very close.
I've been on many big hikes or climbs lately, and when I've returned from the trips, on a couple occassions, I've actually hit the gym afterwards because I still had energy. I would like to think that was because I've been eating and drinking properly. Plus, by doing some light excercise after a big hike, I haven't given my muscles time to tighten. I believe the warm down excercises really help keep the muscles and tendons loose and limber. I am not a runner, I hate running, and I despise pounding my feet on hard pavement. So for cardio conditioning, I stick to various workouts in the gym. Mostly the life cycle, rowing machine, and a lot of raquetball and basketball. But anything will work. Pick a couple things you enjoy doing, and keep at it. Liz (on this site) is a physical trainer and she has turned me on to "spinning". According to Liz, "spinning" classes are 10 times better than life cycles. Another thing I want to start is the stair climber for those steep ascents.
This is what has worked for me. Try a couple things, find what works for you and start with that as a foundation. Slowly, as you find new things, add them to your conditioning arsenal.
And whenever you're ready, you got a ton of guys on here, especially me, that are ready and willing to go on nearly any hike. Big or small, long or short, I love getting out. So if you ever need a conditioning hike, you know how to contact me.
Remember, we're not getting any younger, our bodies are getting worn out, so when all else fails, ask your doctor for 1200mg IBProfin.
~EnFuego