the unfortunate truth is that a nice flat stomach is mostly built in the kitchen, even more so than in the gym.
In my opinion jogging is the best form of exercise for fat loss. I despise jogging because it's so BORING, but to tone up around the midsection there's not much that is as effective. Combined with weight training for increased muscle mass & therefore higher metabolic rate will also give even better results.
As well as this you can do various abdominal exercises (crunches, fitball transfer, hanging leg raise and so forth) to tone the stomach muscles.