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How Do You Organize Your PC Box?

Mine are:
Teams
Sync (stands for Synchronize)
EV'd
Shinies
ShinyLegend
EV'dbyMe
Events
2BeEV'd

Duplicates of some. =)
 
well i use the same team throughout the game, so there's no reason to organize them specially- i just do it by types
 
On Plat I organised by Nat. Dex, I'll do that on HG when I hit 150.
 
In the past I organized by type, but one box was often too small for a whole type. Now I don't organize them at all, except i have a LEGENDS box, a shiny box, and a starters box. I also have a box for Pokemon I'm about to EV train, and a box for my in-game party to be seperated from the rest
 
I'm still sort of on-and-off attempting a living Pokédex in Diamond, so I have my boxes set up 1-30, 31-60, etc. Then I have a box for extras. (Actually, I think I ported everything from 31-80ish to Pokémon Ranch so that I could have two boxes of Cherubi... hmm.)

In earlier gens, I always organized by type. In HG, I haven't decided how to organize things yet. :s I'm halfway through filling box 2 and everything is just in the order I catch it, pretty much.
 
I sort them by type, and normally I pick a matching background too. xD

EX. The Fire box has got a volcano-type background, Grass has a meadow, etc.
 
I have one box for trophies, one box for starter pokemon (all 12 original starters plus the electric pseudo-starters [Pikachu, Mareep, Elektrike, Pachirisu, Shinx, etc.]), one box for my team and pokemon I plan to do something with in the near future, one box for Eevee and all its forms, one box for the masses of duplicate pokemon I get from the pokewalker, and one box for Unown. The rest of the boxes are for pokemon I just catch for the sake of filling my pokedex.
 
In Leafgreen, mine were organized by levels.
For example, one box would be called "Lv 20s" and that would contain pokemon in the level 20 area.
But then this got too hard so I just gave up and threw pokemon in random places. Then that got too hard so I just organized by type.

In heartgold, I barely have any pokemon so ima let that one go for now.
 
I sort Pokemon by type. There is one box though full of favorites or no trades or special Pokes.
 
Right now, all the boxes for all my current games are soooo unorganised. It's really beginning to bug me, and I think I'll take some time later to attempt organisation. <_<;

Legendaries will probably either be alphabetically or numerically organised in one box, while who knows what will go on with the others. Might have to 'borrow' some of the ideas other people have.
 
I don't organize my box in any specific way such as by type, I just put them in Box 1, and when that fills up, Box 2.
 
I label my boxes by what sorts of Pokemon are in it to help me find them easier.

Safari1, Safari2, etc = Safari Zone catches

Getalong = My Getalong Gang (bonus points to whoever gets the reference) which is a group of Pokemon that I switch in and out of during gameplay

InsertNameHere = Box of all the Pokemon a particular person I know has traded to me

Furrets = Box of a bunch of Sentrets and Furrets that I've caught and breeded

IVs = Box of Pokemon with really good IVs - some wild caught some bred

EVs = EV-trained/training Pokemon

The rest of the Pokemon I randomly catch simply land in Box 1, Box 2, etc.
 
IVs- Pokemon with good IVs
EV's - Pokemon that are EV'd
Bread - Bred Pokemon
Random - Some random Pokemon
Shinies - Shinies :D
 
I organize by type, since I can't be bothered to remember their pokedex numbers.
I have one free box for everything else though, and I try to organize all of them by terms of generation and pure types, respectively.
 
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