Simply solution, tidy as you go.
This comes from someone who has stood in front of a bike screaming through gritted teeth that he only had it 2 seconds ago, only to realise it's between his teeth.
So many companies have come up with possible solutions, I'd look at park tools for a start then pop down to your local real bike shop for a chat (be even better if you have a few to talk too), unlike car mechanics they use them day in and day out. I'd better a number of them have some clever ways of keeping track of them (I have a tray that sits on the top tube of the bike when in the stand) and most wont even realise they've done something.
Wera do a full set of coloured hex keys, doesn't make any difference, I still can't find a 3mm when it drops to the floor.
Most now do a T-handled key with a big plastic handle, they are harder to lose but a pain in the bottom to store.
If you decide to extend this to tool organisation please don't suggest foam inserts in a tool draw, It looks great when you only have a specific brand of tool and not a lot of them, when you have 20-30 screw drivers in all shapes and sizes, 20 different sets of plier like items (side cutters, pliers, needle nose, bent needle nose, channel lock, nippers, wire lockers, etc.) 2 full sets of spanners, a full set of sockets, an assortment of bigger items (sorry I got lost for moment) it simply isn't possible in a sensible size chest.
Good luck with it. let us know what you come up with.