On emerald, I arrange them in the national pokedex order. I don't even have half the pokemon, and it's already took a couple of hours just to organize the ones I have. O__o
Organizing your boxes is hard work, man...
I order them by Type. I also have a box for Legends, Eevee (I'm trying to breed one with good IVs and hopefully a shiny), and Unown. Once I get more Pokemon, I may order them by National Dex Order.
I group my boxes by subtype. For example, a Starmie would go in the Psychic box because it's Water/Psychic. For Pokemon with only one type, I just stick them in the box matching their type (e.g. Golduck in Water). When a box gets filled, I simply reorganize it so that all of the Pokemon in it will be resorted into boxes according to their first type.
It's a confusing method, and I've made it so because I was bored.
I leave two boxes open for incoming Pokemon and for duplicate Pokemon, though, so I don't store two of the same Pokemon in any of my boxes and so new arrivals can be sorted later.
I base it on Evolutionary Levels. I have 2 boxes for each. The rest oar for favs and legends. My ;161; and ;162; have 4 boxes. I kept all that i hatched for my shiney.