I actually finished cleaning out my PC recently.
First, I have just some basic Pokemon (Arbok, Togekiss, etc.), organized by gender then by National Dex Number.
Second, I have Pokemon from breeding projects, organized by order of breeding.
Third, next breeding projects, in no particular order.
Fourth, Commonly used Pokemon, like my Ditto, Smeargle, Magcargo, Parasect, Pachirisu, Meowth, Crobat, Vaporeon, and Steelix.
Fifth, I have old ingame Pokemon, like my Arcanine, Butterfree, Blastoise, Infernape, Roserade, etc.
Sixth, my legends, ordered by national dex number.
Seventh, Pokemon that I need to evolve or breed for the Pokedex, ordered by national dex number.
Eight, Pokemon I have received in trades. Ordered by, of course, dex number.
Ninth, Pokemon I am EVing or have been EVed. Ordered by EVed, then EVing, which are ordered by closeness to 510 EVs.
And Tenth, Event Pokemon and shinnies. There are no shinnies, currently, but the Event Pokemon are ordered by date received. Shinnies will be ordered by national dex number.