XY Organizing Boxes

[HoOhLugia]

4 Boxes filled with Shiny`s. 6 Boxes of Amaura that about to release (failed MM`ing)
One box of other Gen 6 (Not much xD)
1 box of 15 Shiny Legends and there normal next to it. 1 other box with random Legendarie. And then the other are filled with eggs or just random pokemons. And 2 empty boxes.

Why don't you wonder trade the Amaura?
Or just give them to me!

Aside from that, I now have a box for Masuda-bred Pokemon including (Oshawott, Snivy, Shinx, Fennekin, Sandile and more)

 

[ScienceBang]

In the start, I ordered mine by their first type, since having doubles would make it hard to organize them via dex number.
It went, 3 Normal boxes, Grass, Fire, 2 Waters, Electric, Dark, Fairy, Dragon, Psychic, Rock, Fighting, Bug, Poison, Ground, Steel, Ice, Ghost.

Next I had some extra boxes, so I put, 1st and 2nd stage Starters in one box,
Then a box for my fully evolved starters,
2 Boxes for Legendaries which I put together based on trios/duos and common attributes (E.g. Victini, Jirachi, Mew, Shaymin are all petit event only legends),
A box for my notably good pokemon/shinies (I dont have too many shinies...),
A box for mega pokemon,
A box for my breeding pokemon,
A box for eggs,
A box for hatched eggs,
A box for wonder trading and getting rid of doubles,
Then I use the rest of the boxes for whatever I want.

 

[Chocolate Death]

I have each box holding pokemon with a specific highest stat or stat.
Boxes 1 - 5 are Attack, 6 - 10 Defense, 11 - 15 Sp. Atk, 16 - 20 Sp. Def, 21 - 25 Speed, 26 - 30 HP.
So far, only 8 boxes are being used though, but I like to also organize pokemon by species and have the ones needing training in Box 30 from the Bank.

 

[Seven is a Color]

I don't organize them at all. When a Pokemon goes in my PC, it just goes in the first available space.

 

[ryter78]

I have boxes of random pokemon that need to or have been trained for pokedex sake. I have a box dedicated to pokemon with good egg moves I come across. A box for dittos. One for having my trained usable pokemon. A box for 'mon to wonder trade (breedables), one for shinies (a whopping 26 open slots), also one for legendaries/ extra megastones, a box ffor foreign pokemon, one for competitive, and lastly some boxes that are place holders while I breed.