Your apt is so cute and fun!
I'm hoping to organize my craft junk in a similar way as you. It's currently in some of those sterelite plastic drawers on top of my dresser in my closet, but the drawers are starting to fall apart! I want to put it all in pretty containers on the tall bookshelf in my bedroom. (Well, all except the fabric and sewing stuff/machines, which live in/on a dresser I've had since I was a baby that is now in my dining nook, lol! That's a whole nother mess.) I think vertically organized is the way to go, since the shelves don't take up a big footprint in my room.