Band-Aids before a long run ... if you're in the middle of a marathon and the chafing sets in, look for the Vaseline at an aid station or the medical tent ASAP.
Another product made specially to prevent chafing is called Body Glide. You can buy it in a cycling or running store.
Avoid cotton t-shirts. Run in a moisture-wicking performance fabric. Moisture is one of the big factors causing chafing and a damp t-shirt rubbing against your nips as you run is a recipe for disaster.
If it's warm enough, just run shirtless. :-)