It's odd how often the question "how do you store your jumper wires" crop up. Naturally, you should be crimping your own but more on that in the future. The best way I've found is to store a selection of wires, sorted by length, on the small cheap breadboards you can get for less than €1. It'll prevent nesting, allow you to easily sort by color and can be kept on the workspace itself for tidy access.
This can also be combined with a utility wall where breadboards can be mounted and then allow hundreds of wires to hang down, easily sorted by gender, length et cetera. Just.. don't cram them all in a drawer, you will regret it.