Crayons never stay "nice and neat" in their boxes in this house, nor do they ever stay in one piece. My solution is the Crayon Can, a huge old coffee can, washed and re-used for over 6 years now.
Colored pencils used to at least make it INTO their box, but they were always getting broken in the process, until I introduced this cheap storage solution -- the Toddler Puffs can. And I'm not admitting how long I've had THIS one! :)