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Pokemon Box system

I have a box just for any HM slaves, because I no longer bother to keep them on my main team.

A box for pokemon in any of the teams I make in game.

In HeartGold I have a box for different teams that characters in the anime/manga/games had. Example, I have a Gary box, an Ash box and a Blue box.

The rest of the boxes are filled with pokemon I caught to complete the dex.
 
I organize them by Egg Group. Makes things easier when it comes to breeding.
 
I arrange them in National Dex numerical order, and then the last couple of boxes are for shinies and fodder.
 
I keep boxes separate for:

- Legendaries/event Pokémon
- Level 100 'mon (or those in training)
- Traded Pokémon
- Shinies

Otherwise, my ordering is completely random. Too much of a bother to shift everything around when I have to add a new 'mon.
 
I never thought of doing it like that really... sounds cool, but what if you run out of room?

That hasn't happened yet. I try to distribute my Pokemon evenly throughout the boxes. If I feel that one box is getting too full, I move a couple mons to other boxes that also fit them.
 
My boxes aren't organized at all.
I'm usually looking for the Pokemon I want for 10 minutes before I find it... :p
 
I have a separate box for my 100s and a separate box for my need-to-evolve Pokemon. Other than that, it's just random.
 
I would organize them by type, like I tried to do with my 2-dozen or so captured pokemon in Emerald, but I'm way too lazy to do that with the hundreds I usually catch. Personally, I love the Gen III box system, plus the additions from D/P. The HG/SS box system is a bit confusing and hard to use for me, someone who never ever uses the touch screen if it's not required, at least not in Pokemon. Also, isn't it stated somewhere in Gen I or II, maybe III, that pokemon are stored as data in the PC (I'm guessing it's Personal Computer?) Storage System?
 
I store them by Nat-Dex order. That's because I used to do just order them randomly, but made the Pokemon I wanted hard to find in Diamond.
 
In White after I migrated all of my others (final evolution of every Pokemon with the exception of only a few) they are in numerical order and then I use extra boxes for Pokemon I have to trade or have extras of and so on.

In Black and the rest I've played I have my boxes go up by levels 10,20,30,so on.. I also include boxes of Pokemon that need to evolve/have HMs so it's easier to find them

For wallpapers.. I do something a little strange.. I have it in the order of the region like in Kanto you start in something like plains, city, forest, crag, river, cave, so on.


THE PC SYSTEM SHOULD HAVE SEARCH LIKE THE POKEDEX!
 
THE PC SYSTEM SHOULD HAVE SEARCH LIKE THE POKEDEX!

They sorta do, you can search by letter, or if you mark them you can search by that.

Well you can in a trade anyway.
 
They sorta do, you can search by letter, or if you mark them you can search by that.

Well you can in a trade anyway.

They should incorporate that into single player and not just during trades. I can't even count the amount of times I've searched through all 24 boxes with a fine tooth comb looking for one poke.
 
In White, I have it by Type, and 5 boxes for the Unova Pokédex. After a new version comes out, and I move all my Competitively-leaning Pokémon over to it, I'll migrate all my National Pokédex from Platinum to White, so I'll have a quick and easy national Pokédex.
 
In HeartGold, I had every box numbering Pokémon - the first box being 1-30, the second being 31-60, etc. - all the way to whatever number Arceus is, because I was trying to catch every Pokémon. In Black, I just have a Storage box (for Pokémon I want to train/evolve), a Shiny box, a Legendaries box, and then every other box is just for random, fully-evolved Pokémon.
 
From the first box, I have them marked "Kanto 1" , "Kanto 2", "Kanto 3", "Johto 1" etc etc until I have the final form of every Pokémon in Pokédex order.
Going backwards, the last box is where I keep my competetive Pokémon and my in-game team. 3 boxes behind that are for event Pokémon, then it's DW Pokémon,then another box for competetive; the gap between that box and my last Unova box are all random.

As for how they are actually stored...it's an odd one, because we've never seen an outside bit to any of the Professor's houses. Maybe they're kept in an underground storage room like battery hens or something? Or like in Oak's house in the anime when they're not outside; kept in their pokéballs in storage rooms.
 
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Can't agree more about going through so many times. Searching by move/level would be GREAT!
 
Legends in the back boxes
My best stuff generally in the front
Everything else comes after them without much, if any, order.
 
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