Running barefoot is more than just taking your shoes off and hitting the track. In fact, if you don't learn at least the basics, you could easily injure yourself. On the other hand, once you get a few technical points down, you'll be running more efficiently and at a lower risk of injury (all without the need for Nikes).
Step 1: The Landing
When most people run, they extend their foot out and land on the ground with their heel. This heel-strike is actually one of the most injury-causing aspects of running. When you heel strike, you are actually stopping your forward momentum and putting a lot of stress on your knees. The heel-strike can also cause plantar fasciitis, which is the very painful inflammation of the (plantar fascia) tendon connecting the heel and the toes. If you've ever had heel spurs, you know exactly why we want to avoid them.
How should we land then? Simple: on the midfoot, or the balls of the feet. In doing this, the calf muscles absorb more of the force than the knee. The is preferable because the calf is a muscle that can be improved and strengthened, whereas the knee is a joint, and extreme pressure on joints can cause aches, sprains, and even tendon tears.
When you land on your midfoot, your stride will be much shorter. This is OK! In fact, a short, choppy stride is what we're after. The balls of your feet should strike the ground underneath your body (see the diagram).