My mat samples are by company, then by color. But only in terms of generalized color groups. A rack usually has whitish/creamy mats at the front, then the 'red' group (yellow, orange, pink, red, brown), the 'green' group, the 'blue' group and lastly the 'gray/black' group. Whites are always in the front, but the order of the groups varies from rack to rack. And within each group, the colors are in no particular order.
Our matboards are by company, and then by number within those areas. Storing them by color alone would drive me up the wall. Speaking for myself only, here, as it sounds like others find it workable. When I cut a mat on the Wizard, I write the number on the leftover scrap and on the fallout right then. It's so much easier to store by number.