DDR3 is, to my knowledge, more energy efficient (as in power saving) and should give you better performance.
When it comes to the X3100 GMA vs. NVIDIA 9400M, it's a no contest: The 9400M wins hands down. While both are basically integrated graphics, the 9400M is seriously a lot more powerful than the X3100. Of course, this is all gibberish if you're not using the Air for anything graphically intensive (and you probably won't be if you're considering buying an MBA).