For weight loss, I always do my training in the morning. Generally if I excercise during the day you, I feel that I am spending the first 20 minutes just burning off the last meal I had, not really burning off stored fat. When I go first thing in the morning, I start burnging stored fat right away. I've read several books that corroborate that, but every book tells you something different anyways.
If you aren't running for weight loss, but you instead you are just doing it for cardio or shear masochism, I'd say its up to you.