I had a lot of "side stitches" when I started training seriously for a 5K, and I got 3 pieces of advice that helped me:
1. Stay hydrated. My running coach last fall said that side stitches are a result of dehydration, and that I should make sure I was drinking about 64oz of water in the 24 hours before I ran. I don't know if any studies back her up or not, but I did find that my side was much less likely to stitch on days when I was good about water, and much more likely to when I wasn't.
2. When a really bad side stitch hits you, stop for a second and stretch it by putting putting the arm on the stitch side straight up in the air, and leaning to the side away from the stitch. I find I have to hold my breath while I do this for it to feel better. That was from my MIL the former nurse and current fitness and stretching nut.
3. Just ignore it and keep going. Also from my running coach. She pointed out that a run-of-the-mill side stitch wouldn't kill me, and that I shouldn't use it as an excuse to start walking. In a couple more weeks of running classes, I found I wasn't getting them anymore. I guess I just outgrew them.