I've got a box for main-game catches (only one because it was a nuzlocke, a box for nuzlocke casualties, a box for catching aids (Synchronizers, Cute Charmers, Suction Cups, Illuminate, Static, Compoundeyes Vivillion with Thief, Sweet Scent Combee, and a Smeargle with False Swipe/Sing/TWave/Taunt. I also shove my Flame Body Talonflame and Pickup team in there), a box for Vivillion patterns and Flabebe colors, a box for my main breeding pairs (this is going to spill over into another box soon, though), a box for pokemon that need their IVs checked and eggs I haven't hatched yet, a box for the ones with 0 in a stat, three boxes for lotto fodder from WT, another box for the 5 IV eevees I've been spamming all over WT, a shiny box, a box for competitive pokemon I'm not using on my team, and my Battle Box, with empty boxes spread around for spacing and future overflow.
...I like organization. It's a librarian thing.
Code: 3136-6781-4024 (Mawile, Clefki, and Forretress). IGN: Tammy. PM if you add! Official Delphox of the Pokemon X and Y boards.
I organize all my pokemon caught/bred purely for pokedex entries by type.
Then I have a separate box for pokemon to be bred (i.e. has good nature or ability, but needs better IVs, or has good IVs but the wrong nature or ability).
One for pokemon with good IVs and the right nature and ability, but yet to be EV trained.
Two (at this point) for pokemon I've completed training and actually use.
And one for "Other" which includes my HM slaves, my breeding slave Dittos, and anything else I want to save, but don't want to be mixed up in the pokedex boxes (like my Sweet Scent Oddish for finding hoards).
The rest are just used for rejects of various types.
Ditto, In Game (in game team and stuff like Sweet Scent Gloom, Entrainment Pangoro), Party (fully bred and EV trained Pokemon), Future Party (stuff I wanna breed at another time), Party (bred, need to be trained), Rejects (stuff I wanna trade), and then everything else
I sort them based on their purpose. Half of my boxes are filled with "Extra" pokemon. Stuff that I don't use and just hold for some odd reason. The other ones are ones that I'd like to EV train, evolve, level up, used for battle, shinies, max IV pokemon, etc.
By colors, mostly. I also have a legendaries box (to be filled when Pokémon bank is available), a box filled with IV bred competitive Pokémon, a box for shinies (this one will be mostly empty... =P have 6 Shiny Pokemon at the moment), and a box almost filled with Dittos for their natures and IVs. I think that's all.
The search feature within the PC makes looking for Pokémon easier anyway.
"I'll show you my superness." 3DS FC: 5172-1017-3752 Pokemon X FS: Poison. PM me if you add me.
I have a box for "my Pokemon" (everything I used in the main game plus everythng non-Kalos that I've trained or use for other purposes), one for my trained Kalos Pokemon, one for things I keep on hand specifically for their use in breeding, and one for Dittos. Then at the other end of my boxes, I have everything that I've gotten from Wonder Trade or plan to trade away over Wonder Trade.