Some of us just pile up the pokemons in the order they were obtained. Some of us arrange them by dex numbers. Some will arrange by pokemon types. How do you arrange your PC boxes?
For me, I have separate boxes for pokemon from the Dream World, legendaries, N's pokemons, and Curtis' pokemons. The rest sort of piles up.
1. Random Pile Box - Usually put in the order they were obtained.
2. Breeding Box - Eggs, Ditto, and other.
3. Legendary Box - Legendaries
4. Shiny Box - Shiny Pokemon
5. N Box - N's Pokemon
6. Trade Box - Pokemon standby for trading and/or obtained by trade
7. EV Training Box - Pokemon in-training and/or to-be-trained
8. Living Pokedex Box - Arranged in the order of the National Dex
9. Type Box - Arranged by primary type
10. Dream World (Females) Box - Pokemon from the Dream World
11. Specific Pokemon Box - Includes having several of the same pokemon like Unown.