Sugars and oils are the big difference. Look at the labels. I prefer Smuckers Natural, ingredients are peanuts and salt. A true natty will almost always separate, leaving a layer of oil on top. The name brands typically add something to keep the oil from separating.
Coop, look above. Making peanut or almond butter really is as simple as ricka182 said. Drop some in a blender and chop and blend until creamy. It will be loud. Some people add a little honey or butter to help things mix and to affect flavor, but that is not necessary.