I bought an old DVD holder at a thrift store for $2. I cut corrugated cardboard to fit in the slots and taped some cardstock to the back side to keep the Spectrum Noir pens from sliding out. It works well for holding the pens flat without other pens stacked on top. That way when I pull a pen out, I can see the slot it came from and put it back. If you stack them in milk jugs or other deep containers, one on top of another, when you pull one out the others that were on top collapse down.
I hope that description made sense.