Here is how I store my Spellbinders dies. I don't have a huge collection and I don't have any grand or border dies so this works quite well. I keep them inside the instructional folder using a small magnetic sheet I've adhered to the inside.
I've trimmed my folders down just a little bit to fit my drawer. Most of them fit fully inside the folder, which protects them front and back and keeps the instructions handy, but there's one or two that stick out just a very little bit from the top. (I keep blank cards and other supplies in this drawer also.)
I don't have enough clearance for dividers but I do sort them into shape groups - rectangles, circles, ovals, tags.