If you have access to tools, it wouldn't be too hard to custom build some simple boxes out of plywood. This will allow you to make them exactly the size that you want, and they'd be a lot more durable than cardboard. Then stain/paint and/or label as desired.
I'm working on a project like this for my 40 or so grolsch bottles, 2 stackable case boxes that will each have individual partitions for 20 pint bottles. I haven't gotten that far with it yet, because I'm making it a lot more complicated than it has to be (sadly, that's usually how I roll). Will post pics when I start putting them together.