Just to clarify a couple of things about mitochondrial DNA:
It is useful as a molecular clock because the mutation rate is known. As far as mutation rate is concerned, the rate of coding sequences is very slow. This is because the selection pressures against mutation in those genes is very strong; cells that accrue mutations in mitochondrial genes will not survive. In non-coding regions, the mutation rate is fast. Slow mutation rate is good because it can show longer term relationships. Fast mutation because it can show short term relationships.
Other bonuses include the fact that there is no crossing over and mitochondrial DNA is, for the most part, maternally inherited.