I’ll post a tutorial about my rigging techniques once this project is done, but I’ll try to explain it here. Basically I have a separate bone for each major muscle, as well as a target for that bone. In the case of the hamstring, the muscle-control bone is parented to the actual femur bone. The target for the muscle is parented to the shinbone and positioned just below the knee joint, next to the shinbone, where the muscle would anchor to in real life. I then apply a stretch-to constraint to the muscle, targeted at the target bone (duh). That way when the joint bends, the muscle stretches and thins out or shortens and contracts, depending on the direction of rotation. I assign a portion of the actual skin mesh to the muscle-control bone, and it now changes shape accordingly.
Hope that made sense! If not, the aforementioned tutorial isn’t a long way off. =)