I arrange them by region, leaving about 3 boxes per region, sometimes less depending on the number. Typically, I don't collect every single stage of each evolution, so it usually works out that 3 boxes is more than sufficient for each region. Of course, for those pokemon that evolve into a different generation, they're moved to that section (ie Johto's Sneasel to Sinnoh's Weavile: Sneasel may originally be in the Johto section, but I'll move it to the Sinnoh section upon evolving).
Then I set aside a box for Legendaries, one for all 12 starters and any multiples I might have (might go into several boxes too), one box for breeding needs (ditto, eggs, etc), and another that contains newly hatched pokemon for whatever reason (currently I have a box half-full of Tyrogue to evolve into Hitmontop since it's pretty much a luck of the draw).
When I start EV training, I'll leave 2-3 boxes for "To be Trained" and "Fully Trained". I'll then use the Fully Trained box(es) for building teams for online battling. That's waiting till Platinum though.
