As with all media encoding, you will trade speed for quality. x264 (ffmpeg) will produce higher quality (or smaller files at the same quality) but will use more CPU. Intel Media SDK should use very little CPU, but the quality will be a bit less. It accomplishes this by using specialized hardware on the CPU, if your CPU supports it.
So, what is best? It depends on want you want to optimize for CPU, Power usage, Quality, or file size.