I sort my boxes as thus;
1-9; Battle; contains my EV-trained non-Shinies. All sorted in National Dex order. They are numbered; box 1 is "Battle 1", box 2 is "Battle 2", and so forth.
10-11; Shiny; contains my EV-trained Shinies, plus one low-level Shiny Pikachu that uses the FEAR strategy. All sorted in National Dex order. Also numbered- "Shiny 1" and "Shiny 2".
12; To train; contains the Pokémon I intend to EV train. I also use it to temporarily store certain Pokémon that I intend to otherwise make use of in the future, such as a pair of Wobbuffet I intend to breed, my cousin's Panpour I'm going to trade back to him, a female Jigglypuff I've been using for Cute Charm, and a low-level Bagon to make use of the Repel trick during Wynaut swarms. Currently houses the six Eggs that will hatch into my Black 2 team.
13-15; To trade; contains the Pokémon I keep as trade fodder, such as Dream World females, leftovers from breeding projects, extra legendaries, et cetera.
16; Eggs; contains leftover Pokémon Eggs which I trade away over GTS negotiations. Ideally, I trade an Egg for another Egg. It's fun trying to guess what might be in the one you recieve.
17; Natures; contains my Synchronizers and my various foreign Ditto for the Masuda Method.
18; Events; contains my event Pokémon, such as an extra Mewtwo, two Ash's Pikachu, two Japanese Pikachu-Colored Pichu, and a bunch of the Shiny legendary gerbils and Celebi from GameStop. Also contains a few Pokémon I consider to have stupendous sentimental value- the Patrat and Lillipup that were my first two captures of Unova. Also a formerly Shadow Croconaw and a Smeargle with Reshiram and Zekrom's signature moves.
19-21; Reserves; contains the Pokémon I rotate on and off my in-game team. Usually they're from Pokémon games past, but there are some exceptions. They only go into rotation if I've really bonded with them.
22; Unown; houses my Unown collection, sorted in alphabetical order. Aside from the collectibility, I use them as a "keyboard" of sorts on GTS negotiations when I want to convey something specific to the other guy. For instance, this one guy tried to pass off his level 3 Mewtwo and a Shiny Chimchar in a Dream Ball, so I used my Unown to spell "SCREW YOU HACKER" and promptly disconnected on him.
23-24; Legends; houses my legendary Pokémon, sorted by National Dex order. Only one of each. They're numbered "Legends1" and "Legends2".