On Ruby I store them randomly (though I do try to put the evo chains together), and on my other games I store them by number, which is an option I think you missed on the Poll.
I also use some boxes for organizing the Pokemon that I want to train, or Extra parties. I also use them for the Pokemon that I normally breed, and sometimes I use them for Getting more of Pokemon that aren't found often, such as Articuno. AND, I use them for creating my Army of gengars, so I guess I'll chose random...
I have it sorted by type,cause in Ruby I'm going to vs.Winona(sp?)and I go to the Electric box and Rock box and take out most of those pokemon(It makes it easier to find them that way)
National Pokedex order makes Pokemon easiest to find, especially if I've been busy looking at a strategy guide and want to check out the stats on one of my Pokemon. Then I have an extra box for those worthless Unowns.
I usually sort them by Type, Legendary, and Pokemon that I want to Train/HM Slaves.
In my Emerald, I traded over so many Pokemon from other games that I had like more than one box for normal pokemon, and more than one for water, and it started to get to cramped. I just decided to jumble them all together, and put all higher level pokemon in one box. I mainly have boxes like .. Pokemon I train, Legendaries, then like 4-5 Boxes of Pokemon that I have bred to have amazing movesets/natures that people might want from me, and the rest are just garbage.
I have a weird way of sorting my Pokemon. o_o I have a box for my party, I have box of Pokemon from other games like FR/LG, Colisseum and XD and then I have 4 boxes of random Pokemon from Emerald. XD I really need to sort my Pokemon. I'd like to sort them by type, but's there's not enough boxes. *should buy Pokemon box*
Boxes for types, one for former team members in case I decide to bring them back, one for legendaries and a last one for things I have more than one of.