5th Gen Amanita's PC!

It's funny that Gen V is the first one when I actually arranged my Pokemon within the PC boxes. XD

If I remember correctly, I've got two boxes for Pokemon that would complete my Pokedex. The second box has specific ones that I actually caught due to liking them, yet not enough for me to add them to my team.
Another box contains my hatched Pokemon, each being grouped in one line within the box.
And then the fourth box that I use contains my HM buddies. This occasionally becomes the box where members of my main team temporarily stay whenever I need an HM buddy. To sum it up, I have four PC boxes in use at the moment...and yeah, I haven't finished the game yet to use more.
 
I name my boxes after types. Not all the types fit so I pair a few like Dark/Ghost, Rock/Ground, Bug/Grass, and Ice/Water. I've always organized my boxes this way though. :)
 
I have the following boxes, though it's the first time I've actually renamed and used them to classify my Pokémons:

Favorites: all in the title, the Pokémon that I prefer, and need to store from time to time

Evolve: Pokémon I captured and need to make evolve in order to complete my Pokédex (since I'm pretty early in the game, still)

Done: well, the Pokémon that can't evolve anymore :classic:

Dream: Pokémons I got from the Dream World

xx Pouinks
 
They need more boxes. How are we ever gonna get all 629 pokemon with 8 boxes?

You'll get more boxes if you put a Pokemon within all 8 boxes, then when you press back and switch out of the menu, it'll add another 8 boxes. Then fill those with at least one Pokemon and you'll have all 24 boxes.~
 
  1. n00bs ** This is the box I close on. It's sort of a carry-over from GenI/II, where you couldn't catch Pokémon if the active box fills up. I keep it empty unless my other boxes are bursting at the seams, in which case it handles overflow. I just hate newly caught guys ending up in the wrong boxes :P
  2. Norml/Fly ** Type specific boxes. Mostly untouched or incorrectly trained to evolve for Pokédex purposes.
  3. Fire
  4. Water
  5. Grass
  6. Electric
  7. Ice
  8. Psychic
  9. Dark
  10. Fighting
  11. Rock/Grnd
  12. Bug/Poisn
  13. Ghost
  14. Dra/Steel
  15. Legends
  16. Promo ** Includes anything from Mystery Gift, tickets, or DW.
  17. Breeders ** High IVs, males with useful egg moves, and foreign pokes I plan on breeding shinies of.
  18. Stock1 ** Mostly Lv1s with egg moves, starters, and other things which may be valuable for trades.
  19. Stock2
  20. Synchro ** Filled with Synchronize Munnas in different Natures arranged in a grid. +stat along the X, -stat along the Y. The remaining column contains Dittos with useful Natures.
  21. OMGSHINY ** Non-EVed shinies
  22. NU/UU ** EVed guys expected to belong to these tiers
  23. OU/Uber
  24. Staff ** My ingame team and slaves

If I run out of room in my stock or breeder boxes, I can collapse more of the type boxes into combined ones. At least we don't have to worry about Pokéradar this gen! I have 5 chained shiny boxes on Pearl!
 
I have LOADS of full boxes called 'Pokemon' and 'Pokemon2' and 'Pokemon3' etc.
But for my main ones, I have 'Rares' for legendaries and just rare Pokemon, 'DreamWorld' for Dream World Pokemon and 'Temp' which stands for temporary, which is where I put my Pokemon that I don't have room for in my party (ones I'm training basically)

-totodile42
 
I have 2 boxes full of EV trained, battle-ready pokemon (without items, of course), these are back in my boxes behind my legendaries, my dittos, and a box which has useful synchronizers and pokemon I need to EV and train to 100, along with my flyer.

The first 10 boxes are full of pokemon caught over the last couple generations, in case I need them to breed and train, for an egg move, or for pokedex filler.

I also have two boxes of pokemon valuable for either their egg moves, or female DW pokemon. Then I have one with some eggs which I didn't feel like hatching.
 
I have a sort of organized chaos theme. I know where everything is, but there's no rhyme or reason to it.

In other words, it's too tedious and I'm too lazy to properly organize them.
 
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