I still have intermittent problems with my back, feet, and shoulders from long hours. Some of the things I find that help my body recover the most are:
1. Heat. If you have access to a jaccuzi, use it! Soak until you feel like you will melt. Some people swear by epsom salt in addition, but it never seemed to make any difference for me. It might be worth a try for you nevertheless. If you dislike the idea of a bath, a heating pad or hot water bottle can help, but a long bath works best for me.
2. Pills. I dislike pills in general, and so I reserve them as a last resort, but sometimes being sore can create additional problems beyond just the annoyance. If I'm extremely sore, I'll take a pain reliever/anti-inflamatory or two before the bath. The name of the game is letting your body relax as quickly as possible so the built up tension doesn't cause any additional problems. I can't sleep well if I'm very sore, either, so if it's bad enough for me to need a pill or two, they will help in allowing me a decent night of sleep as well.
3. Stretch. Works best after the heat treatment. Don't bounce, and don't push your body until it really hurts, just gently stretch (if it's already quite sore, yes, it will hurt a bit, but it will feel MUCH better afterward) the parts that are sore for prolonged periods to help keep knots from forming in your muscles.
4. Regular exercise. Like cypressrider, I found that walking or jogging regularly helps a lot, but that bored the piss out of me, so I took to hiking. I have some friends who I hike with, and I can at least take some pictures and spend some time in the relative wilderness if going solo. Exercising in a way that you enjoy more makes it less of a chore and easier to keep doing.