Minneapolis maker Greg Flanagan made an organizer for his tools using a slab of CNCed wood. First he arranged the tools how he wanted them. Next, he took a photo of the arrangement and pulled it into his vector art program where he traced the tools. Finally, he imported his drawing into CAM software and carved it with a CNC router.
The reason I always disliked this general way of storing tools–often seen as pegboard with the outline of each tool drawn in Sharpie–is what do you do if your tools change? This way you can just output a new organizer. Love it!