I often organise my boxes, but it depends on the game. In my Platinum, I don't have a lot of Pokemon besides my main team, so I just keep all the Pokemon that are not in my party in one box.
But in Diamond, for example, I have LOTS of Pokemon, so organisation is crucial. My boxes 1 and 2 are for Pokemon I'm training right now. (In this game, I'm leveling up a bunch of Pokemon equally.) However, I'm keeping my better Pokemon in box 1 and the less likely ones to be used for beating the E4 in box 2. The Pokemon that used to be on my training list, but aren't anymore, are in box 3. Box 4 is an Unown box; it has all 28 Unowns in it. Boxes 5 and 6 have Pokemon that aren't in the Sinnoh dex. Box 5 has Pokemon that are on my training list; box 6 has the miscellaneous Pokemon. Going backwards, my last box holds my HM slaves, Pickup slaves, my False-Swiping Sneasel, and my shinies are at the very bottom (I currently have three). The two boxes before that hold Pokemon I've caught for the sole purpose of showing them to the News Centre in Solaceon; one has Pokemon below level 20 and the other has Pokemon at or over level 20. The box before that is a "baby box"; all the Pokemon are level 1. I have one box with nothing but baby Aipom and Pachirisu in it, for some odd reason... Then I have another box with Spiritomb babies and eggs, another for Feebas babies and eggs, and another for miscellaneous eggs.
In Emerald and Leaf Green, I have a special box to hold the Pokemon I intend to trade inbetween GBA games, or migrate to DS games. And in Sapphire, I have a box for all my contest Pokemon, and a special box for the eight or so Pokemon that make up my "best team".