We love colours in Montessori. In Montessori 6-12 classrooms, we have a couple of ways we sort things. We try and sort shelves from left to right with the easier activities on the left. This helps the child see the progression of where they have come from and where they are going towards.Shelves are also arranged by curriculum area. While ideally, we want to use natural materials it is also helpful to label materials to help children know where things go. In my mainstream class I have a Montessori colouring system to help students know where things go.
I have used small 'sandwich' plastic containers to store some of my materials. I bought a whole lot of these so I can swap them around if need be into other curriculum areas. I have labelled them with a colour coded circular sticker and then a label to explain what the material is to help with children know what they are doing.
In this picture, you can see some of my history boxes. They have a black dot for history and then a label saying what is in each box. The stack on the left are fundamental needs through time, the stack on the right are the different geological periods.
I love using natural materials too below these things on the shelf I have a basket with the timeline of life materials in it.
Some of my other materials are kept in laminated manilla folder pockets. In this picture from my old classroom, you can see my Botany (Green) and Zoology (Red) resources, some of which are in baskets.