Usually it's just ankle pain. I slipped a tendon about 6 years ago and it never got fixed, but I've been managing ever since then, and it's not as bad as it has been in the past. Also, I have Achilles tendinitis that flares up from time to time, but it's better if I just constantly wear legwarmers.
When I do modern, I sometimes have to deal with my wrists in pain because not only am I managing carpal tunnel syndrome in both wrists(I am also an avid knitter), I broke my left wrist 6 years ago(on stage during a pas de deux lift gone horribly wrong), and I will probably be dealing with arthritis because of it in the near future(or so the doctors say).
I used to have knee issues sometimes, but not lately. I really have to watch out when I demonstrate that I turn out from the hip and not the ankle, that's when I feel it in the left knee.

I have a lot less pain when I am working on recital stuff because I don't have to break down new steps and demonstrate full out so much.