Organization?

[Wigglytuff FTW!]

I've organized my boxes by type in every game except Pt., well, in Pt., the only organization I have is seperating legendaries, special babies with spevial moves, and eggs I'll be trading to HG.
But I might steal coolespeon's idea and try to organize by color... meh, I'll figure it out.

[GIR7590]

I sorta organize them... I have two boxes for my main Pokemon, one for all the special ones, one that I'll trade to SS when I buy it and one for the Unown letters, and the rest are just stashed in random locations.

[foxyman1167]

Lets see on my current Platinum file, I have them in different boxes for different regions, but only fully evolved.

[LadyMiir]

I sort by levels for boxes 1-6, 7 is for my Legendaries/events, 8, 9, and 17 (don't ask) are for normal Pokemon received in trades, 10 and 11 are those up for trade, 12 is starter Pokemon; 13 is Eevolutions/Eevees in general; 14 is GTS Pokemon; 15 is for those Pokemon I have already bred for trades and set aside as "reserved", 16 is spillover, and 18 is my "fighters".

[Dehydrated]

I organize it all by type. That way if I want a Water Pokemon, I go to the Water box.

[Xylon Uxkid]

I always keep my favs on the last boxes (17-18) and the others in random boxes.

[blaziken#1]

type. pair up grass/bug rock/ground ghost/dark if it 2 types then whatever i want it in
once in the right box then do it by lv
sometimes i need 2 boxes for water and grass/bug

[Uber-Rocky]

I organize via National Dex. I only have the final evolved forms of pokemon, so i have so many boxes like 1-50, 51-100, 101-151...etc. Then I have a 'battle' box with my team pokemon, shiny box, ingame pokemon box, trading box

[kiwi-kauri-kid]

BOXES 1-5...
These boxes are in regional order, holding- not surprisingly- tgeir regional Pokemon, in Pokedex order.
The box wallpapers are kind of coordinated to the region kandscape, too- Kanto is grassy, Hoenn is underwater, Sinnoh is snow (because of the mixed enviroment, and I prefer the snow to the others) and Johto is simple, because I haven't played through there yet.
5 boxes= too many Kanto Pokemon.

BOXES 6/7...
After recieving *coughstealingcough* Pokerus from a friend last night, box 6 is now allocated all my Pokerus'd Pokemon, excluding legendaries/my team. There's currently about 5 of them in there.
Box 7 is my 'Tradeable' Pokemon- Pokemon that I have more than one of *looks at Eevee* or my friends have requested (IE Ditto).

BOXES 16, 17, 18...
Box 18 is full of Unown, which are simply ordered alphabetically, box 17 holds 'Others', which are legendaries (in the order that I captured them) and my team/pending team.
Box 16 is for Pokemon Eggs, which is normally rather full due to my mates and I spamming te Egg Spin function of Platinum.

[chimecho_guy]

I organize by type!

[Byzantine]

I put the ones I use in two boxes, shove the rest into like 5 or 6 boxes, put shinies in 2 boxes, legends in 1 and ditto in 1 (The legends overflowed into the ditto recently).

I used to organize them by type... Then I ran out of boxes.

[Agonist]

i have 5-6 boxes full of ev'd pokemon, another 5-6 boxes of smogon redistributable stuff/breeds of mine, and random stuff in the other boxes

[cannibaleyes]

Haha, my PC is pretty scattered. I do have a few boxes that are organized, though. I have a few boxes dedicated solely to shinies, and others dedicated only for EV-trained/IV-bred pokes. Other than that, I pretty much just throw things in whatever box. It's starting to get annoying and hard to find things, but I'm too lazy to go through and re-organize it. =/