I'd recommend having a look in the "Identified" and "Unidentified" forums here as well - without the ability to use DNA from family members (even generations apart) many sets of remains would never be identified. The maternal line is important because it's always consistent - I have mitochrondrial DNA from my mother, who got it from hers, who got it from hers, who got it from hers and so on, and it remains largely unchanged. While males do have mtDNA, they don't pass it on the same way, but they do inherit it from their mother. An example of this was identifying the remains of the Romanov family (the last Russian emperor) executed during the revolution. The Empress Alexandra and her children were identifed using a sample from Prince Philip - his mother's mother was the sister of the Empress.
It's also the reason why most breeding (horses, cattle etc) traces lineage through the female line.