I use large zip lock bags.
The gallon size bags can hold several smaller (eg, quart) sized bags, allowing one to organize via caliber or platform, with subdivision bags going in the bigger bags. There's usually a place to write with a Sharpy so you know what's inside specifically, in addition to being able to see and feel. The magazines stay dry, and can be placed in boxes for hard sides if desired.
The zipper is much better than the "press/squeeze" type.
Freezer bags are a bit thicker gauge, so hold up a bit better to sharp edges. But if a bag rips beyond service use, a box of new bags is not expensive.