In reply to girlymonkey:
Calf raises might help but I would be cautious about trying that first as you might agravate the problem. Whenever I have been advised to do them by a physio they have always suggested only training them eccentrically. Normal running, especially anything fast or uphill will train your calves concentrically quite enough. That kind of concentric training is usually prescribed after recovery not at the beginning of having a problem. If your issue stems from overuse or the function of your calf muscle being hindered by another issue then training it with calf raises is putting extra strain on something which is already hurting - not a good idea. Eccentric loading may well help but it still causes stress to the muscle so I would go easy with it and not use additional weight until it was healed.
The other things that have helped me are isometric stretching and self administered myofacial release. Some people seem to be able to achieve the latter with a foam roller but for me the best way I have found is to dig my thumb into the muscle and then flex my ankle back and forth. If you're tender already then the goal isn't to hurt yourself with it but it is quite uncomfortable. Isometric stretching is very easily achieved with the calf muscles by standing on a step and letting your heel drop into a stretch then activating the muscle to raise yourself slightly out of the stretch, holding and then releasing back down and repeating. Best performed after the massaging as you will increase your range of motion. As others have said you can experiment with different degrees of knee felxion not just with a straight leg. The position of your toes has an effect as well, if you have an incline board (or a bit of wood on some steps) then you will notice the extra strain by having your toes prevented from curling down.
In my (limited) experience most muscle pains are caused by a problem somewhere else, quite often that muscle making up for an imbalance, weakness or tightness somewhere else. The only way you'll fix that is by seeing a good physio. Your body should be capable of doing what you're doing with flat uncusioned shoes as long as you build up to it slowly and don't have any pre-existing conditions which the extra strain might bring out.