When I was at The Container store (great place, btw), I had some time to kill and wandered around various sections, zeroing in on the small boxes. They have so many kinds, different designs and a wide range of prices. That’s when my eye caught the Infinite Divider System boxes (by Flambeau). They look like your typical multi-slot segmented plastic boxes used for crafts (where lots of little bits & items need to be organized). The “Small” box (in between mini and large) is just about perfect for pens & pencils. The slots have numerous fine grooves along the sides so you can very precisely set your dividers. The plastic quality is excellent – really thick and sturdy. Plus the hinge is a real hinge, not some bend in plastic that will eventually break. I got one to try out and I’m going to pick up a few more.
Can’t wait to see how you utilize these. Storage and display is, by far, the trickiest thing I deal with with my collection.
I also collect and build guitars. Those are easy to store and display. Not the case (npi) with all of these darn pencils I have.
As I have only one of these, I just crammed in a bunch of pencils & pens I had lying around loose in a single box. I’m thinking of getting a few more. One channel I might divide up to store lead.
I’m currently in the process of building my own pencil storage. Well, technically my own storage inserts. i have some acrylic cases that are meant to store jewellery but the supplied dividers leave a bit to be desired, so i’m planning to create custom dividers out of wood and cover them with some type of soft material. I’ll post pics in a separate thread when i’m done.
You could flock it. All you need is the flocking, the color coordinated glue and an applicator.
Here is a pencil tray I made and flocked.
Here is a YouTube video that describes the process.
Nice!
That’s flocking awesome!
What the flock!
It’s flocking St. Patty’s Day green! 
I see people are flocking to this post!
I’ve been meaning to ask how your storage system is working out