My legs will be sore after a long ride, but generally that's it. I used to have problems with lower back, neck and shoulder pain but increasing my flexibility and fixing bike-fit issues took care of that. I do find that I need to stop and get off the bike for a few minutes after 20 miles or so, or else my mid/upper back starts to feel stiff from being in one position too long.

If I do weight training the day after a long ride, I will notice less strength in my upper body, so those muscles are tired from the ride, but they generally don't hurt.