Box organization.

I only tend to capture Pokemon that I think I'll use in my team at some point or another. Because of that, over the course of most games, I'll probably end up with about 20-25 Pokemon in total (including gift Pokemon). Hence: no need for pesky organization! Woo hoo! I can't even remember the last time I used any other Box than numero uno. :D
 
I organize boxes in terms of level, and stats. If I deposit my highest leveled pokemon, I would pit it in the first slot. But if I deposited a pokemon with greater attack, that pokemon would take the first slot.
 
I usually just put the Pokemon I like to use (or the legendaries) in one box, then the random ones I've captured as dex fillers in another. I'm also really organized on my White version, where I keep all of my IV bred/shinies etc for trading.
 
I organize by type : Box 1: Water. Box 2: Fire and so on and so forth. The Pokemon in each type box are then sorted by lowest level to highest level.
 
I've always been compulsive about placing my 'mons in the boxes that resemble the place they would live in the wild. I also have a box for my team and the ones I've EV trained. I also have close to 4 boxes full of unhatched eggs.
 
I would organize it by type and then have the boxes labeled legend and eggs. And like Plumpyfoof does i give them the correct wallpaper. Then I would start to move them and in a week i was right back where i started. But now that i'm going to get more into competitive battling i might label them breeders and EV/IV Trained.
 
I only oraganize some boxes for the pokemon that I use for battles. I put my legendary pokemon in one box. I put pokemon eggs in one box so I can hatch them later.
 
I used to be super anal about my boxes, organising them by type and then by level within the boxes. I'd also have one for breeders and legendaries. Now that I'm working on my National 'Dex I've just shoved them all in randomly because I was taking out and putting in Pokemon really frequently and it got too time-consuming.
 
Meh. Sometimes I try to organize them but end up getting lazy and not keeping it up to par. I usually try and make the boxes based around how much I like the Pokemon. So there are names like, "Beloved" "Cherished" (for the original team I use to beat the metagame) "Cool." I may also create "Legendaries" "For Trade" "Unevolved" "HM Slaves" lol
 
I once organized my boxes in my Sapphire game, one for each type. While, in every other of my Pokémon game, I don't mind about the organization at all. My boxes are just a bunch of Pokémon, some important, some randomly caught...
 
I have a box for party pokemon, Eggs, and legendary, Rest are organized by type, of course there's never enough boxes for each type so I combining types since I keep at least one of each. Think I've used 2 boxes for normal type.
 
My PC, starting from Black, will always have the following boxes: Legends, Teams (for Pokemon who are or will be trained for the purpose of Competitive Fights or Battle Facilities), and Specials (filled with pokemon that I cherish so much, either some old teams I use during past games, event pokemon or those that I really like to keep.)
The rest of the boxes are only for the Pokemon I catch whenever I try to complete the Pokedex

during Soul Silver, I have special box filled with Unowns, One for each letter of Unown. I even showcased it in the Global Terminal, Soul Silver.
 
I place Pokemon in numerical order, then I have some boxes for other purposes, so up until Box 9 (Gen III), Box 12 (IV) or Box 15 (V) there will be a box for the all the Unown, Ditto (Natures), Egg Move fathers, Hidden Ability (Gen V only), Event, EV Trained, Shiny and Special' which would contain my in game team and others that I would never get rid of. Spare boxes are just named 'Other' I usually put Pokemon in there that are pending to be traded (Gen V only).
 
I organize my boxes as to which kinds of Pokemon should be in there. I named a box "100LEVEL" and stuffed it with all my level 100 Pokemon.

Another separate one is for legends, which I named "LEGENDS", and so on.

I have 12 organized boxes in total. But I gotta say, the "LEGENDS" and "100LEVEL" are my most favoured boxes.
 
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