My mats are always disorganized. I have sorted them into color families, and have drawn a line along the bottom for each color family. Then each successive color family has a slightly higher line on it. Then when I do un-disorganize them its a matter of lining up the lines and does help me to resort them fairly quickly.
Takes around 1/2 an hour to resort the mats, but only takes minutes to get them out of order!
As to dividers, I don't use them anymore. I had some from my distributor, then I cut some from matboards, then I just dicarder them completely!
I have however also lowered the central board that the mats rested on so that the mats now sit slanted. (Does this make any sense?) With the mats slanted and angled I can see a 1/4" of the faces and can see the color of the matboard.
I like the marker method, also.... Different colors at different levels on the edge of the mat sample (no marker on whites). Keep the marker side facing you, not the customer, and they'll think you're very good at what you do.
Yellow, orange, red, purple, blue, green, brown, black, and a silver or gold for all the metallics.