Side stitches are one of running's great mysteries. They affect many people differently, and many not at all. Kind of like hiccups. Here's a few good articles on them, which include some remedies. Personally, I'll take a few strides (10-15 seconds worth) with my arms raised over my head to help "stretch" the muscles and areas in the abdomen. Overall, it's an effect of breathing and the internal organs/muscles/ligaments and them cramping up.
You'll have to experiment as to what works best.