My system is similar to Kathy's, except that I don't keep my samples and my folders together.
I have my folders in a plastic bin that is sized for CD's - the folders are taller than that, but the width is good and I'm fine with them sticking up. Each folder is labelled with it's name and they are sorted in alphabetically order. I did my samples on file cards, with the name and manufacturer written on each one. Punched a hole in the corner, and they are stored on a ring, also in alphabetical order.
I saw this system from someone else either here or online somewhere, but unfortunately I don't remember where. I like having the samples together to flip through, and then just pull the folder(s) that I want.
Who needs tattoos? I already have ink in strange places...