Terrible Stomach Aches

I would look to what you are eating in the hours prior to the run.  The slightest little indigestion can extrapolate big time when you are running.  Try to experiment with different pre run meals to see if it goes away.

What kind of nutrition are you using for the run?

Oh yeah I forgot all about that.  The nutrition you are using WHILE you are running is just as important as what you eat beforehand.  

I was having the same issue with runs over 6 miles and I happened to mention it to one of the swim coaches.  She suggested cutting out any dairy the night before or the morning of my runs (my long runs are usually earlier in the day).  I paid attention to what I was eating and realized I was eating a bowl of cereal and drinking the milk left in the bowl every morning.  When I stopped doing that and eating oatmeal or a cliff bar instead on those mornings I had no issues whatsoever.  
As the other posters mentioned, it could also have something to do with your nutrition during the run. 

Dehydration can cause stomach pains/cramping. Are you hydrating properly before and during your run? If it isn't your diet I'd guess it's this.