The Pie Family
The Pie family includes, but is not limited to, Granny Pie, Pinkie Pie, Marble Pie, Limestone Pie, Maud Pie, Cloudy Quartz, Igneous, Gummy. Does not include the Apple family.
The Cake Family
The Cake family includes, but is not limited to, Carrot Cake, Cup Cake, Pound Cake, Pumpkin Cake, Pinkie Pie, and Gummy.
The Sparkle Family
The Sparkle family includes, but is not limited to, Twilight Sparkle, Night Light, Twilight Velvet, Shining Armor, and Cadance, Flurry Heart, and Spike.
The Royal Family
The Royal family includes, but is not limited to, Celestia, Luna, Cadance, Twilight Sparkle, Blueblood, and Discord.
The Belle Family
The Belle family includes, but is not limited to, Rarity, Sweetie Belle, the parents, and Opalescence.
The Apple Family
The Apple family includes, but is not limited to Apple Jack, Big Mac, Apple Bloom, Granny Smith, Breaburn, and any other named or unnamed member of their large family. Does not include the Pie family.
The Dash Family
The Dash Family includes, but is not limited to, Rainbow Dash and, in most cases, Scootaloo.
Fluttershy's Family
Fluttershy's family includes, but is not limited to, Fluttershy, Angel (and all of her other animals), Zypher Breeze, and her parents.
Multi Family Focus
Multi Family Focus is where you will put stories where two or more families are largely the focus, such as a story where the Pie family and the Apple family have one big reunion, since they might actually be related. This also is where stories where two of the Mane Six decide to start a family together.
Other Families
This is for other families, like Derpy and Dinky, or Tunderlane and Rumble, who probably wont have enough stories to warrant their own folder. In the event that a particular family does get enough to have their own folder, it will be created. (I'll set the threshold at twenty-five for now).
Mother Celestia
Any stories where Celestia is seen as a mother. I'm honestly a bit uncertain about this folder, but I suppose we'll see how it works out.

These are the most likely characters to appear in the family stories, but if there is one where Rarity and her cousin have a spa day or Dash and Fluttershy talk to their parents, they go into the folders for those families.