I second the caffeine BIG time.

But if I have to run on an empty stomach, I have a serving of my Infinit Nutrition sports drink a few minutes before I head out the door. For running, my solution has 256 cal/20 oz and 1.5gm of protein. So far, this has worked well with my stomach. If my run is over an hour, I'll carry a half serving with me as well. The liquid has been better for me than even a gel.