I found a great design on Printables by JsR for a modular bike stand tray for tools. I printed just the main tray and a side cup to hold some of my most-used supplies for bike maintenance. The bottom of the tray has many screw holes in it to add more compartments around the sides of it.

One surprising trick I learned with this print is that a corkscrew is a great way to get the supports out of a small, delicate screw hole. It has just the right amount of sharpness, ability to get in small spaces, and leverage.
