There's a couple of these systems out there, but they are either proprietary or based on Fusion 360. For these and a few other reasons, I designed my own system. I'm also more of a coder than a designer, and one of the things I love the most about FreeCAD is that it's possible to build things in code.
Because of this, my system has always been macro based. But not everyone wants to go muck with code, so I've figured out enough Qt to stick a GUI on the front. This macro lets you generate system grids and boxes in any size you want (although the bigger it is the slower the generation time). There's checkbox options for basic blocks that control features like a scoop at the front to make it easier to get parts out and a grip/label holder at the back.
You can also get a box with no front face, and I've just added an option to generate a sketch that fits the inside profile of a box, as a starting point for custom boxes. I'm going to work on some custom blocks next (tool and bit holders, etc.)
It's all AGPLv3 licensed and available on GitHub at https://github.com/instancezero/in3dca-freegrid. I'd love feedback, bugfixes and contributions.
Script for generating 3D printed storage boxes and grids
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Re: Script for generating 3D printed storage boxes and grids
Sample end product, grid with magnets and a divided box.