Could a sleeping bag be warmer if you are naked inside? I have heard conflicting theories about the best way to keep warm in a sleeping bag in the winter.  Some people say you should bundle up in your sleeping bag and another theory says that you should be naked, because the warmth of your body will create a microenvironment of very warm air right next to your skin, since the sleeping bag and pad reflect heat very efficiently, and there is no way you will get that warm if clothes block contact with the air.  Does this "naked" theory make any sense according to Physics?
 A: short answer: No, the more insulation between a hot body and a cold body the slower the movement of heat from hot to cold.
long answer: If the clothes themselves are cold then bringing them into the sleeping bag requires them to be heated as well as the air/skin (which is what produces the warm feeling), so short term, go naked, long term keep dressed.  
A: Let's start by assuming the sleeping bag is perfectly reflective and impermeable to heat, and that your body remains at a constant temperature (which it generally will unless you're very ill or in danger of dying from being too hot or too cold).  In this situation, thermodynamics tells us that everything inside the sleeping bag will eventually come into thermal equilibrium with your body, reaching the same temperature as it. When this happens you will feel nice and warm (if not too hot) and will not be losing any heat to the outside world.
However, the time taken for this to happen is very dependent on what's inside the sleeping bag with you.  If your clothes start out cold and have a high heat capacity then they will have to absorb a lot of heat from your body before they reach its temperature, which will take time. So if your sleeping bag is a perfect insulator then you should definitely be naked, because that way you'll feel the benefit of the sleeping bag more quickly.
However, even a very good sleeping bag isn't a perfect reflector of heat and will let a little bit of it through, especially if it's very cold outside. In this case the temperature will still reach a steady state, but it won't be a thermal equilibrium.  Instead the system will reach a state where your body is constantly emitting heat, at a rate that's balanced by the rate at which your sleeping bag leaks heat to the outside world.  The slower the leaking of heat, the higher the temperature next to your body will be.  Your clothes are insulators and slow down the leakage of heat, so in this case keeping them on is a good idea, even though it will take a while for you to feel the benefit.
So I guess the tl;dr version is, you should be naked if your sleeping bag is very good and/or it's not too cold outside, and/or you won't be there for very long.
A: The relevant issue is that the clothes you wear (unlike the down or synthetic fibers of the bag) hold moisture next to your body. Changing both the thermal conductivity of the medium surrounding your skin allows energy transport to the environment. The evaporative heat loss dynamics of the body-bag system is described by another thermal conductivity. 
I propose the effects of creating a moist fabric layer allows a more efficient heat flow from the body than an air insulator. Water transport through your fabric should be best in your sleeping bag, naked a should feel colder and you will freeze in wet cotton cloths.
A: Physics occasionally misses human experience. When we get cold, our hands and feet become frigid while our torso and heads1 stay relatively warm. Our bodies' tendency to reduce blood flow to the extremities is an evolutionary adaptation to the fact that high surface area to volume things (such as hands and feet) radiate heat faster, and we can survive without fingers, but not without brains and hearts. Unfortunately, this trend also self perpetuates; we must feel warm for our bodies to allow blood flow to return to the extremities, and our hands and feet occupy a proportionally large portion of our sensory cortex2.
If we are naked in the sleeping bag, there are no layers of insulation keeping heat from our hands and feet. Further, if we put socks on in the sleeping bag, we may be insulating our feet from the warm air inside the bag. If you are truly cold, get your hands and feet touching the warm parts of your body.
If you are warm when you get into your bag, dress however you want - be comfortable, and if your bag is rated for the temperatures, get those hopefully not too wet clothes into your bag to warm and dry. 
If your bag is not rated for the cold temperatures, a layer of clothing may insulate your torso from the cold enough to survive the night, but your feet and hands will be frigid. They will also have a difficult time figuring out what is wet - problematic for all the reasons mentioned in the other answers. I'd strongly consider putting your clothes under your torso to supplement your sleeping pad - if your body touches the ground through the pad, you lose way more heat to the ground through conduction than the air through blackbody radiation. If your clothes are wet, under the pad is a better option, though you will be pretty upset in the morning when you try to put them back on.
The last things to remember are more personal. If your sleeping bag is tight around any part of your body, you will get less insulation there. More clothes could exacerbate that unless you're wearing a girdle. Smaller people in bags that are too large should definitely put their dry clothes below their feet to fill up some of that space. The shape of a sleeping bag is very important, and if your toes aren't near the end, they will get cold.
Having done it both ways, I'd rather bring just enough clothing and too much sleeping bag on any trip ever. Being cold during the day is part of the game, but a lack of sleep because of cold will ruin you.
1 Heads radiate quite a bit, but they also get us out of trouble, so our bodies don't shut down circulation to them.
2 See sensory humunculus, possibly nsfw, and yes, google, humunculus is spelled right
