General

I generally split them into pokemon I'll be breeding and the finished ones. Some boxes are randoms like wonder trade boxes and 1 box dedicated solely for breeding gibles.

PC Box:
- Many boxes organized by type
- 2 boxes for breeding including eggs
- Shinies
- Legendary
- Vivillon and other form changers (kyurem fusions and so on)
- Junk box

Just for the heck of it I made a Magikarp box.

i organize them by competitive use
-wall breakers
-walls
-stallers
-support
-spikes
-spinners / defog
-wish washers
-doubles offensive support
-doubles defensive support
-gimmicks

then breeding use
-ditto+whatever i need for breeding that sesion

then the event mons
then the legendaries

the rest is trash by type

[quote=pinksinsftw]6 boxes of shinies, 7 for[b] breedjects[/b] for breeding, 1 for Vivillon, and 17 for Masuda breeding and stockpiling for WT.
And one Battle Box.[/quote]

Breedjects! Now I have a name for one of my boxes.

I used to organize my boxes by type but once I got shiny fever, I only cared for shiny hunting.

I have my first two boxes dedicated to Kalos Pokemon, stuff that would be legal in online competitions and such. My utility pokemon like Vesiquen (sweet scent), Tropius (4 HM moves), and Talonflame (Breeding and Flying) are also in there
Box 3 is my work in progress box with either pokemon I'm trying to breed for IV/nature or shininess.
Box 4 are random shinies I have caught/traded and extra Yveltal, Xerneas and Zygardes I got from the GTS.
Box 5-6 are a bunch of dittos I caught in my safari. I have every nature on them so I can breed the correct nature to any breedable Pokemon.
Then I got my Battle Box with my standard team.
Behind the Battle Box I got 2 boxes of Legendaries, organized my Generation and number.
Before that I have my Starter box, with all the Starters 5-6IV, some shiny
Before that I got my Event box with Gen 6 Event pokemon like Vilvillon and the new Pinsir
Before that there is my Rain + Sun team pokemon, organized by weather and ability (Drought, Chlorophyll, Flower Gift, Harvest, etc)
Than there's my Sand/Hail teams, arranged in the same fashion as my Rain + Sun box
Then I got my Gen 1-5 Special Attackers, from Choice Specs, to Nasty Plotters
Then it's my Gen 1-5 Physical Attackers, with Setup attackers first and 4-attacks after that
Then it's my Stall/support team members, with Baton passers, Wish Passers, Healers, Screeners, Entry hazards, Phazers, and Status-users arranged accordingly
Then it's my Mixed attackers like Salamence, Electrive and such with Bulky pokemon like Gastrodon, Slowking, and such.
The remaining boxes are for breeding rejects, Pokedex fillers, and random Wonder trade stuff.

All my boxes are useless DNA produced by breeding

6 boxes of shinies, 7 for breedjects for breeding, 1 for Vivillon, and 17 for Masuda breeding and stockpiling for WT.
And one Battle Box.

I have one box for pokemon I care about(starting team/bred teams) another box for pokemon i use for IV breeing and then the rest I don't care about.

i sort them by type. fire, water, grass, fighting, flying, dragon, etc. if they have two different types then i just use the first "main" one.

also i sort legendaries together and shinies together.

Once I get enough Pokemon I'll usually sort them by number, and then I'll have separate boxes for my trained pokemon, shinies, etc

-pokemon I use
-pokemon I don't use

by types

Pokebank:
All pokemon by National dex number + all their forms.
All pokemon by National dex number + all their forms shiny.

Main game:
Battle box - Main VGC style team.

Rest of the boxes:
Attackers, special attackers, stallers, set up and bulky.

Box 31:
Breeding box with all Dittos and eggs.

LOL organization. I organize them the same way I do anything:
stuff them in a container and hope I find later

i breed a lot of pokemon for nature in sapphire then I stuffed them in each box and released most of the weaker ones.

i don't really do any real ordering. the only real organizing i do is making a box specifically for eggs and stuff. but i don't hvae pkmn XY

[quote=ilikefoodand]The order I catch them in b/c I don't have time to organize them.[/quote]

Pretty much this for me.
Back in the older games--Gen 1 to 3--I actually use to bother with arranging things by their 'dex numbers.
The most I usually do nowadays when it comes to arranging things is having a box specifically for my Shinies.

The order I catch them in b/c I don't have time to organize them.

too many to actually sort, mainly i have shinys, legendaries then everything else

I don't! I don't care nearly enough to sort my Pokemans. Plus, you can tell their EVs/IVs just by stats, so sorting them is just more work.

I sort them by type. Then I have use the remaining boxes for pokemon I've ev trained/iv bred, event pokemon, dittos, and random.

Divide my boxes half for collection/trophies and other half for competitive pokemon.

I suppose I should have expected another wave of pokemon hype now (I honestly get tired of hearing about it with how many separate threads basilers make).

Well last time I played pokemon (like 6-7 years now), I arranged them by type, and that worked out pretty well. Seems like you'd have a lot of extra space in some of those boxes arranging them that way, but whatever makes it easier for [i]you[/i] to locate a pokemon works lol.