I have made a few wood trays, but I am not so happy with them, too heavy for one thing.
From my searches I have found that jewelers use standard size utility trays for storage and display. The standard, or full size, is 14 3/4''L x 8 1/4''W and comes in heights of 1", 1-1/2", 2", etc.
These trays use inserts depending on the type of jewelry you want to display. They also sell plain pads that fit inside, some of them velvet covered.
What caught my eye is that there are jewelry supply houses that sell these trays for less than $2. each! There are inserts, that is tray liners, made of some thin flocked plastic, available for the trays. None that I have found are a perfect fit for pens, but some come very close. Look at:
http://www.nilecorp.com/products.asp?sku=97%2D05
These come is several colors. Two of these inserts fit in one standard size tray.
A regular tray and two inserts costs less than $3.
One drawback is that jewelry supply houses have minimum orders. Most of them about $100.
Look in Nile's catalog for Utility Trays and inserts.
Anyone selling other small items can also get inserts sized for keyrings, bottle stoppers, etc.
If you happen to look at these, please let me know what you think.
EDIT ADDED:
Look also at http://www.nilecorp.com/products.asp?sku=1732%2D1
These are acrylic pen displays at $4. each !