Initially, I organize my boxes either by type, level, or evolutionary status. I like to change the wallpapers so that I have a box for each type, but I quickly get sick of organizing, and my system falls apart.
On Diamond, I have a number of boxes for different purposes, but I didn't start out with any sort of master box organizing plan. I have several boxes of miscellaneous Pokemon that I caught in the game, several boxes for bred Pokemon (they used to contain lots of Squirtles and Bulbasaurs that I bred before learning how to RNG, but I finally moved a bunch of those to My Pokemon Ranch), a box of legendaries and events that I obtained myself, several boxes of other events, a couple of boxes of shinies I traded for, a box of shinies I RNGed, a box with starters, two boxes of Dittos, a box of GTS traded Pokedex fillers/alternate ID numbers, a box (or half a box) of "junk" Pokemon to trade away, a box of egg move Pokemon, and a box of frequently used Pokemon (HM users, extra team members, my Magcargo and Camerupt for hatching eggs, etc.).
My B/W games are currently sitting in an Amazon box at home, waiting for spring break to start, so I haven't worked out my organizational system for them yet. I suspect that I'll probably have a system that's similar to the one I have in Diamond (though I probably won't have a chance to trade as much as I did when Diamond came out). I don't plan on transferring too many of my old Pokemon to B/W, aside from newly hatched Pokedex fillers (or, potentially, freshly bred team members).
I'm glad we have more box space, though it makes sense given that there are more Pokemon now. I just wish we had even more box space (maybe even an infinite amount). I don't want to worry about catching too many Pokemon, and I hate releasing Pokemon.
