Perhaps one of the more surprising tricks for organizing art supplies that I picked up in design school was the importance of making color charts.
Color charts save you the time and the hassle of searching for the perfect color for any given project, and this in turn can prevent quite a bit of mess. I used to lug my entire selection of colored pencils or markers to my drafting table. The problem with such an approach is that my work area would be piled with supplies I didn't need, making for cramped conditions. Nowadays, with my color chart in hand, I pull out just the supplies I need; it's easy, fast, and it ensures that I have the colors I want and the room I need in order to work.
Color charts also help prevent costly mistakes in buying art supplies, as you can bring your color chart with you on shopping trips to determine your purchases and avoid buying unintended duplicates.
Lastly, I've found that it's especially useful to use a color chart as a kind of where-to-find-it guide, in that I put my supplies in the same order that I use in my charts. Not only does this enable fast selection, but it is especially helpful for those supplies--such as pastels and colored pencils--that lose their labeling with use. I love my Prismacolor pencils, but after sharpening a few times, good luck knowing what color they are, as the color code quickly gets whittled away. The box the pencils came in is handsome enough, but doesn't stipulate what colors go where. I just use my the color chart I made as my what-goes-where guide, and am never at a loss for finding a particular color.