How do you organize your pokemon boxes?

I sort them by levels, then have some boxes for my rares, team, and my pikachu.

I have mine by theme and picture :)

So I have a beach box that is called "beach" with the background and then things like Wingull, Krabby, Spheal.

I like it when things are organised!

I have all my Legendaries in the back, then in Box 1 I just sorta put stuff in there for now.
In box two I have all my Pokes that I beat the E4 with, whenever they aren't in my team.
Box 3 is nearly empty, and Box 4 has a bunch of Chimchar I was breeding trying to get a specific nature. Box 5 has my Competetive pokes in it, or atleast in progress pokes... Then box 6 has the monotype team(s) I've started on building just for fun.

I always have a shiny and legend box. I used to organize by types but now I bust can't be bothered.

I usually organize them by types. It makes it a lot easier for me to navigate.

Type. I've rarely bothered to organise my boxes though. It's only when I've completely conquered the game and have nothing else to do that I start collecting Pokemon.

In some games, I have one of each species and put them in pokedex in order. In other games, I only have final evolved pokemon in pokedex order in my pc as well as boxes for my baby pokemon, shiny pokemon and unown forms.

Once I can see the National number on the stat screen, I go by that. Otherwise I use regional numbering, however, I only organize at all in Gens III and IV. It's too hard to do before that. I use Box 14 for alternate formes, duplicates and events. (I'm still hoping for Pokemon Box D/P)

1-493

I will catch em' all!!!!

And the last box is for multies

well I raise all my pokemon - except unknown and ditto - so I have my boxes ordered to make this possible.

starting with box 18. this box I name "NEWBIES" because I make sure I close the pc in that box. so, when I catch a pokemon, it goes there and I can sort it from that box into the box it belongs in. I put this box in box 18 so that I can see boxes 1-6 at one time (when you move boxes, it shows six at a time up top, you know).

the rest of my pokemon I organise into boxes 1-6. see a pattern there? yeah, there's six pokemon to the party. so I take one pokemon from each box and that's my party. I put my pokemon in the boxes based on typing. so in each box, one type matches the other types for that box because the two types are close, etc.

when a pokemon in my party levels up I replace it with a lower leveled one from it's corresponding box. that way, I raise all my pokemon at once at all the same level.

------------------------------------------------

MY BOXES:

1. psychic, ghost, dark

2. rock, ground, steel, normal, fighting (the last two I had alone in box 6 but then I found I needed a lone box for the flying-types so I put them in this box and the flyings are alone)

3. water, ice (only if they can surf. if they can't, they're probably dual typed so I put them in another box (i.e. smoochum box 1. all pokes here have to know surf. surf is an important hm so it always needs to be in my party)

4. grass, bug, poison

5. fire, electric, dragon

6. flying (all pokemon here can fly, another important hm. all flying types are dual typed so if a flying type can't fly I put it in its other type's box (i.e. natu box 1, mantine box 3, etc)

-----------------------------------------------------------

there's more. I use the next six boxes, 7-12, for "DONE" boxes. starting at lv 20, every five levels I have the option to stop raising a pokemon in box 1-6. but that's only if the pokemon has fully evolved. if it had not evolved at say lv 20 but does at lv 21, I still have to raise it until lv 25. then if I want to stop I can put it in it's corresponding "DONE" box (these are orgainized just like boxes 1-6).
.
for example, mr. mime Really annoyed me. but I couldn't stop raising him 'till lv 20, at which point I gladly put it in the done box. another example: my beedrill. it's pretty weak and at lv 20 I thought about getting rid of it. but it wasn't a total fail like mr. mime; I could bear with it for another 5 levels until 25, at which point I'm thinking I'll probably put it in the done box.
.
my goal is to raise every poekmon as long as possible. every five levels I'll drop a few into the "DONE" box, and narrow down to my stronger ones. by lv 40 or so I plan to have six good, solid, strong pokes in each box. I don't think I ever want to get smaller than six per box. it's a good veriety and makes the game worth playing to lv 100!

anyway, for the other five boxes in my pc. I don't really use them for too much. well, maybe I do. one's a totodile box in which I put all my baby totodiles (I started the game with a female totodile, lucky me :D, so I made a bunch of babies for trading purposes (I need those version exclusives, etc that I can't get in the game on my own). oh and my ditto, for baby-making use. so it's like a tool box, if you will. another box is for the 24 unknowns I've caught (don't have ! and ? yet). another is for junk pokemon that I accidentally catch in the safari zone or bug catching contest or get in trades, that I use for the nice people who trade freebies :D. and two boxes I just don't use.

that's it!
.
.
.

I have type boxes in SS. If a box gets full I just put some of the dual types in the box corresponding to their other type.In DPPt I just throw my Pokemon in any box.

Before GenIII, I stored them as I got them, but then started storing them by type, but was not given enough boxes, so in GenIV, I either store as I get them, by type, by color, or my most recent idea, by level, so my strongest pokemon are easy to find.

Hmm..
Well,for me it's sometimes organized by type or if their a starter or the area their located in.

I've always organized them by type.

I have a designated box for my Grass types, all the others are just random junk I've picked up along the way =P

Haha. Maybe once my collection builds up a little more I'll try a little harder to keep things more organized!