heres mine:

box 1-3: wild pokemon i have obtained in sinnoh and have no use of training
Box 4: are in game "pokemon league" battlers
5: HM slaves other useful (such as slugma to hatch eggs)
6: pokerus - common pokemon who posses it, so i will always have it
7: train - special pokes i plan to train/EV train and use in battle
8:wifi: pokemon for trades i have organized
9-11: trades - either wifi, link, or pal park pokes
12: battle - my various wifi teams
13: same as 1-3
14: rare - hard to get pokes, such as version exclusives or fossils
15: DADDIES!!! - um... some dead beat dads... and mom's as well.
16: BABIES!!!! - orphans... free (not really) to a good home
17: MORE!!!: more orphans!
18: legend: all my legendaries.

my shinies also go in 'rare,' but theres only one, and he gets his own special corner!!!

1-4 babies ( me lika the breeding ) 5-8 moms and dads then pokemon for the wii battle revolution in 9 the rest just mixed together

I usually organize them by types: Fire box, Water box, Grass/Bug box, ... and my legendary box

back in RSE, i arranged the boxes by type.

in DP, its just a mess of pokemon in each box

There all random except for a box thats filled with my Feebases that I tried to get shines out of.

I organize by type, combining some - like Grass/Poison and Fire/Dragon - for types that don't need the space. Then I use the extra space for special pokemon - like an OU box, an Uber box, and 2 shiny boxes

I organize mine by first Type and the last one is things im Ev training.

i organize mine by type. and if they have two types i catagorize them by their first type. except for flying. any pokemon that has flying as one of their types i have a special section for them. and i also have a legendary box for all my legendaries.

First... 5 - 6 boxes are chock full of shinies from when I used to collect them like a madwoman. Never had the heart to release them since they may prove valuable one day. Next box is for random, in-game pokes that don't have a place elsewhere in my PC. Then I have a few boxes specifically for my event pokemon (JAA, Movie Darkrai, various Mews, PBR Pika, etc.) and then a "SLAVES" box for HM Slaves, Magby, and Dittos.

I have another box for pokes with egg moves, another one for pokemon that are ready to be EV trained but are untouched, and two more for pokes I've already EV trained and are ready to be used on Wi-Fi. I have a "trophies" box for random legends with good natures that are really just for trading as I'll probably never use them.

Hard as I may try to be organized, though, I have random, unhatched eggs littering the entirety of my PC. >_< I'll need to sit down and just hatch all of them one day so they'll stop wasting space...

wow - am i the only person who organises them like this?

BOX 1: 1-30
BOX 2: 31-60
BOX 3: 61-90
.
.
.
etc

with the last box and a bit of box 17 with battling pokemon.

ok, i do have another game which is more random. it has shinies and traded pokemon, as well as a few boxes with breeding stuff (some dittos, a camerupt, etc).

All of mine are just in random boxes. The only one that's actually organized is my Fail Box. That's where all uneeded baby pokes go. When the box gets full, I throw 'em out and put my breeding pokemon back in the daycare.

i used to do that too!!! i think my new system is better though

Box 1 - Firsts : Usually the first Pokémon I catch at the beginning of the game as I'm going through it. Later used as a catch-all storage box for stuff I want to keep, but not necessarily train.

Box 2 - Potential : Pokémon that I'm in the process of training and/or want to eventually train.

Box 3 - Main : My main team, plus any other I've trained to competitive levels.

Box 4 - 2ndaries : My back up teams and any other Pokémon I find interesting and/or have a soft spot for (like my F Annon)

Box 5 - Babies : I don't breed alot, so my babies are kept here.

Box 6-7 : In Diamond, I'm using these as ID Number boxes for Trades. Pokémon that I'm keeping solely for Lottery purposes.

Box 8 - Fossils : My revived fossils, :B

Box 9 - Legendaries : My Legendary box.

Box 10-11 - Brood : My breeding box of mother/father Pokémon. Usually untrained and just used for breeding stock.

Box 12 - Experiments : Any baby Pokémon that I do a mass batch of wind up here. Generally useful for competition, I still can't seem to give them away, ~.~;;

And the rest of my boxes are full of Trade Fodder. The first five boxes are pretty consistent with all of my games though (Firsts, Potentials, Main, Secondaries and Babies), and the rest vary from game to game...

I've had my boxes organized by type in this order since RBY. GSC made it even easier to find PKMN because you could see the picture.
1psychic
2poison
3bug
4flying
5fire
6water/ice
7electric
8dragon/water/ice
9fighting
10normal
11rock/ground
12grass
-------end RBY
13dark/steel
-------end GSC
14steel
15ground
16ice
17ghost
18extra
-------end PD
But I have so many Pokemon now that I just squeeze them in the 1st available spot.

All my boxes are in order

Normal Pokemon
Ghost/posion/dark
Bug/grass
Water
Ice
fighting
rock/ground/steel
pshycic
legendary's
shiny's
electric
flying

So on

I have 2 boxes set for the extra's i have and eggs

Mine is like this :
Legends
Eggs-(Would type the egg's number in Comp. and save to remember if hatched would transfer to it's respective box)
Kanto- 3 boxes
Johto- 2 boxes
Hoenn- 2 boxes
Sinnoh- 3 boxes
Team
and some random boxes

I do the same as Cuddles Numerical order I have all the pokemon in the dex Except Arceus and Shaymin. The last box is rares shinies and my team snd my original e4 team an infernape and alakazam lol.

I organize mine like this...

Box1:Amazon
Grass/bug/Normal types with level below 90
Box2:Volcano
fire and fire combinated types with level below 90
Box3:Nautilos
Water type with level below 90
Box4:Desert
Ground/Rock/fight types with level below 90
Box5:Darkness
Ghost/dark/psychic types with level below 90
Box6:Sky high
Flying types below lvel 90
Box7:Mecanix
Electric/Steel and some others(Like porygon) with level below 90
Box8:Mountain
Some others types like dragon and other rare pokemon...
Box9:Egg-Ditto
I put all my dittos and eggs here...
Box 10 to 12:Lv-100 B
I put here all my pokes in lv:100 except legendaries and ubers
Box13:B-Shinies
All my shinies i caught using pokéradar with my OT and 100% legit.
Box14:H-Shinies
All shinies i got on trades and don't know if they're hacked...
Box15:Legends
All legendaries and Ubers
Box16 to 18:Nameless
Where i put the rest...

In RSE & FRLG they were according to type. In D/P I put them in order according to their national dex #. It took forever, but it helps me keep track of what I need it pretty cool.

I organize mine by type.

to me

organizing, smorgizing my bokes. no really i never organized my boxes

I just put pokemon of similar value/usefulness together.

My battlers share boxes, my non battling legends share boxes, my 31 iv pokemon group together based on species, and all my usable hatchlings do the same.

As well as all the bordline useless pokemon they're all together too.

I'm running out of space tough):

i organize mine by type, but there aren't as many fire types compared to grass, so i might infuse the fire box with something like rock.