I was thinking about organizing lego too - at the moment we keep ours in big plastic storage boxes, all piled in together (one for Duplo, one for regular lego). Even the small models have ended up mixed in. Only our son's Jack Stone set stays in its big cardboard box on his request.
Playing with the lego with the kids one day, I thought that perhaps searching for the pieces they want helps with their spatial recognition skills - you know, identifying the shape among all the others, when it is upside down or whatever. (or would learning to organize be better? ;-) I'm thinking of just using a small divided plastic box to organise the really small and 'technical' bits, but leaving the bigger pieces loose in the big box.
cheers
E.