Here's how my Platinum boxes are set up.
Box 1: "For trd." Was originally supposed to be a box holding the pokemon I was supposed to trade, but it is now full of random pokes.
Box 2: "Random 1". Read the box name. Very random.
Box 3: "Random 2". Same as above.
Box 4: "Random 3". Same as above.
Box 5: "Legends". Used to hold all my legendary pokemon, from Mew to Arceus.
Box 6: "EVd OU". Held my EVd OU pokes for a while.
Box 7: "EVd UU". Held my Ambipom and my Raikou for a while.
Box 8: "EVd NU". Never held any pokes it was supposed to, since I don't have any EVd NUs.
Box 9: "EVd NFE". Nothing.
Box 10: "Latias :D". An entire box full of my favorite pokemon, Latias, forming a heart.
Box 11: "Trade2SS". A bunch of pokemon holding items that i'm going to trade to SS as soon as possible, since i'm making SS my main game when I get it for... a LOT of reasons.
Box 12: "TrdToSS2". Same as above. Continuing from the last box.
Box 13-Box 16: Normal names. Just random pokes in these.
Box 17: "Giveaway". This box held the shinies I gave away for free (well, almost, I took a few Explosion TMs for them since I have an european platinum, and i'll therefore get an european SoulSilver too) in the trade center a few weeks ago.
Box 18: "Shinies". This box used to hold my shinies, but my shinies are getting sent to SS, so they're now in the "Trade2SS" box.
That's my box system for ya. Very messy, but I don't care. I find my pokes anyway. xD