The best thing is alot of riding without stirrups. It is really helpful if you have somebody that can lunge you while you practice, especially at first, so you can concentrate on yourself. If not, then you can do the same on your own, just make sure you aren't pulling on the horses mouth. First work on it at the walk, then sitting trot, rising trot, 3-point canter, and then finally 2-point. It will take a long time to get there, but once you do you have a really strong seat, balance, and more strenght in your legs.
You can also either drop the reins or hold them in one hand, and do exercises with your arms while you are riding. Like putting your hands on your hip, shoulders, arm circles, hold them over head, to the side, in front of you. Just about anything you can imagine.
There is a book called Fitness for the female equestrian that has some on the ground exercises in it that might be helpful. I'm not at home so I can't look at it right now, but that would be another place to start.