Amy's got the right idea. The clear totes....
My daughter(6) has totes in her room the huge ones that you would store like winter clothes in or whatever. And each storage tote is labeled Barbies, Polly's, My little Pony's, BabyDolls, Bratz and so on. My daughter can only have one out at a time too and clean up is a cinch. This also keeps the toys from mix matching because if they mix all their toys in one toybox they start to miss pieces and then really don't play with the toys at all. If your trying to make this look pretty you could always decorate the totes, paint them or something.
As far as art/crafts I'm doing this as my daughter's xmas present. I bought a utility banquent style table from Menards, then went to walmart and bought those storage carts on wheels that have several drawers. And I went nuts with art supplies that's my daughter's "Art Center" She is gonna love it, she likes to art stuff more than anything and it's all going to be done at her table all organized every crayon, marker will have a home etc. That was my idea to get her stuff off our kitchen table.
With books we have thousands, I did try the whole book shelf idea for awhile but then it got messed up all the time or it looked so nice and neat she wouldn't go grab a book to read and because we have so many books I finally just threw them all in laundry baskets on the floor. I have them seperated right now in a basket she can read by herself and harder books into another basket I have to read to her or she will grow into. It's all completely accessable to her and she can't make a mess.