I was over at my friend's house and she had a great way to organize her brushes and paints. She hung the tubes from binder clips and stored the tools in hanging glass jars. They are all out of the way but still easily accessible. This same technique could be used for markers, pencils or any type of craft tools and supplies.
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I use two types of containers to hold my fancy paper. I like those stacking plastic "drawers" from the office supply store. They are made just the right size to hold reams of paper and I wait until they go on sale for half off (for about $15-$20).
Full pieces of construction paper can be stored in file folders or in those magazine storage boxes. You can also spray paint cereal boxes to put your paper in.