The Marilyn Monroe boxes were a gift and I store my brushes in the last box. I keep my everyday makeup in the middle box and small things (cotton buds, cotton pads, swabs, etc) in the top box. I usually keep the perfume I am currently using on top so that it is convenient. On the right, you can see that I try and keep my brushes neat so that they do not lose their shape.
I found these ideas online and I thought they were clever!

Using old jars and filling them with beads (source)