I use lots of pokemon through the course of a game, so I'm constantly rummaging around in my boxes, rearranging my team.
Going from the first box to the right, I sort by quality, subdivided by special or physical if necessary. The first box is the first string pokemon - the ones I know I can count on - then it goes down from there, all the way to the junk I know I'm never going to use. Going from the last box to the left, I have duplicates, things I'm going to breed, things I've bred, extra eggs and babies and so on. Somewhere in the middle I have boxes for stuff I want to keep but am probably not going to use - preevos, shinies, legendaries, events and the like.