I typically just reserve one box (usually the very last one) for Pokemon which I've levelled up significantly, be it previous party members which I've replaced, or current party members for temporary storage. I also keep unique, single-encounter Pokemon, such as legendaries, in the final box, usually lined up in a row towards the bottom of the box. When I tried my hand at breeding for a while in Pearl, I also had another box for eggs and newly-hatched Pokemon. Otherwise, all my other Pokemon are just stored haphazardly starting from box 1.
Lately, however, I've never really captured enough Pokemon to fill even half a box, so organizing my Pokemon hasn't been an issue.