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Living Pokèdex. Box 1: #001-030, Box 2: #031-060, etc. it gets tricky though once you hit Unown, and all of the alternate formes after, the numbers get screwed up obviously.
Interestingly enough, in BW2 there are 24 boxes and you're able to hold a max of 720 Pokémon; including all alternate formes, there are 727 Pokémon, but 7 of those formes aren't available outside of battle or to put in the box (3 for Castform, 1 Cherrim, 1 Shaymin, 1 Darmanitan, 1 Meloetta) so there are exactly 720 to put in boxes, it works out perfectly.
If only we could have both Kyurem formes at once though. Sigh.
