Regular peanut butter, as in most famous brands and store brands, are made with ground peanuts, sugar, salt and partially- or fully-hydrogenated vegetable oil. Ringing any bells? It should. Hydrogenated vegetable oils (also known as trans-fats) are chemically changed to make the liquid oil solid but this process also makes them so bad for you that they're on the very apex of the food pyramid, just above deep-fried Snickers bars. Peanut butter itself is actually rather good for you, with a good amount of protein and a little kick of iron. Adding trans fats just to make it shelf-stable kind of defeats the purpose.
Natural peanut butter has that layer of floating oil on top because it has not been chemically (read: toxically) altered. You should see that as a good sign. The natural oils in peanut butter are unsaturated and, like olive and canola oils, can actually help to lower levels of bad cholesterol and raise levels of good cholesterol. Most natural peanut butters are made only with ground peanuts and a little salt. Some have extra oil added to make the butter creamier; some have sugar added. So what if you have to stir the stuff up with a knife before you use it. Would you rather have some doctor scrape the gunk out of your arteries?
Reduced-fat peanut butter, by the way, is a total scam and you should avoid it at all costs. Like other reduced-fat imposters, fat (in this case, heart-healthy fat) is replaced by sugar. But your body will turn that sugar into fat right away so it's completely pointless. You do your body a disservice to substitute good fat for bad sugar.
By making your own peanut butter you can strictly control what goes in the stuff. And it's really, really easy. First, buy yourself some shelled, dry roasted but unsalted peanuts. If you can only find salted they'll work but it's better if you get to decide how much salt goes in the butter.
Dump your peanuts in a food processor or blender and whir until you get a thick paste. If it's too thick you can add a little peanut oil. Add salt to taste. Put the peanut butter in a resealable plastic container. If you plan to use it quickly go ahead and leave it in the cupboard but if you think you'll take more than a few weeks to devour it, then store the tub in the fridge.