pick a dog with a natural build, and one that isn't known for hip/knee problems. a dog with an easy gait. short haired. a dog that requires very little grooming. a dog with low prey drive, that doesn't bark at every squirrel. not hyper, but plenty of energy. a breed that isn't known for obediance difficulty. and train the dog, obediance school will more than pay for itself.
german short haired pointers, weimeraners, vizslas... all make great trail dogs. so do mutts, chosen well a mutt can make a fine trail dog
http://www.youtube.com/watch?v=Lif6o8iE5cA one of my favorite thru hike vids, with a fantastic vizsla