I sort my Pokemon by National Dex Number.
So if I hypothetically had one specimen of every Pokemon, it would start with Bulbasaur and end with Arceus.
If I also had one copy of each forme of a Pokemon with Alternate Formes, I'd order it like this:
Deoxys: Normal, Attack, Defense, Speed
Burmy: Plant Cloak, Sand Cloak, Trash Cloak
Wormadam: Plant Cloak, Sand Cloak, Trash Cloak
Shellos: West Sea, East Sea
Gastrodon: West Sea, East Sea
Rotom: Normal, Heat, Spin*, Cut*, Wash, Frost
Giratina: Another*, Origin
Shaymin: Land, Sky**
*I prefer the forme's Japanese names, so as such I'll use them. For those out of the loop: Spin = Fan, Cut = Mow, Another = Altered
**Since Sky Forme Shaymin cannot be put in the PC, I'd have one Shaymin with the Standard Land Forme's Moveset and EVs, and another with SKy Forme's standard Moveset and EVs.
As you can see I'm very methodical about PC organization.