Yes, it tones your legs very well (running and jogging at least. I don't sprint so I don't really have much knowledge as to how anaerobic activities such as that effect muscle composition). And while running doesn't necessarily tone your upper body the same way weights do, it burns fat quite well which exposes the muscle beneath it, making you LOOK much more toned, and that is what is important
. Same goes for abs, though I think running directly tones them more than arms. But the elimination of belly fat dramatically effects the look of the abs whether the running itself builds muscle there or not.