The Three Great Royal Families first appear in User:Otherside86's fan-made season finale two-parter The Royal Families. The families are the most powerful force in the universe. Each family has a responsiblity to maintain balance for all of existence, for better or worst.
Princesses Celestia and Luna are members of one of the Great Royal Familes. Them and their cousins must do their part to keep balance to the world. Their families is charge of ruling over different parts of the earth and protect the lifes that are in it. Celestia and Luna were choosen for the duty of moving the sun and the moon, ruling both the night and day. They both became the rulers of the new found land Equestria, and are the only known alicorns there. But beyond Equestria, in other parts of the world, their other relatives rule their own kingdoms and take care of the ponies who live in them. Two of Celstria's cousins, Lord Thanatos Embermane Darkfire and his brother, Phantasm Cadaverous, are the rulers of the Underworld. Darkfire attempt to destroy Equestria, as in his dark nature. But he is now sealed away in Tartarus, under the watchful eye of both his brother and Cerberus.
Another family is in charge of ruling the cosmos. Traveling far to other galaxies, and keeping balance in other planets and stars. One member of the family, Prince Comet, has a romantically relationship with Princess Celestia. But the two know they can't truly be together become of their royal duties.
Time and Space
The third family is unique for the power of time and space. They have the ability to go to different eras of time and travel into other dimensions. They are trusted with the duty of mending ripples in the space-time continuum.
The counsel families began long ago, long before Nightmare Moon, with three of the most powerful families of alicorns. In the lair of the counsel, there is a great hall with three-massive walls, each with the family lines painted on them. A few of the relatives are painted in a big golden star that shows which family members are eternal. Some relatives are given responsiblies that are forever, and are given the power to live forever. Such as Princess Celestia lifting the sun, or Lord Cadaver guiding departed souls to their proper place. Not all the relatives can live for an eternity, yet most of them do start families of their own. Some get married into so many pony families, that their descendents are born as different kinds of ponies. Some are Alicorns, Earth Ponies, Pegasi, and Unicorns; like Princess Cadance and Prince Blueblood. There were a lot of disappointing descendents over the years, Blueblood was no exception.
Long ago, all three families banded together to defeat a great threat far beyond all others. If this old foe would've have return to endanger all existence, they will need help from EVERYONE in their familes.