I have a full set of imperial bits - fractional, lettered and numbered - that came in a metal bit file. I reserve those bits exclusively for use in wood. The fact that each bit has a dedicated place means that it's easy to find specific bits for an application.
I also have a random bunch of standard jobber-length twist bits that I have purchased over the years or inherited from my dad or FIL that I keep in two plastic boxes that originally came from the deli and contained sliced, baked ham. One box holds bits 1/4" and smaller, and the other holds larger bits. This setup is a bit more difficult to use, but it works for me. These are the bits that I reserve for use when drilling metal.
Then I have another of the plastic boxes that I use for specialty bits - brad point, 'aircraft' length, etc. I have fewer of them, so finding the bit that I need is not a problem.
And I have another plastic box (we're big on ham sandwiches in our house) that contains spade bits. Don't use them often, but sometimes they are convenient to have.
I bought a set of forstner bits at the big box store - 1/4" through 1 1/2" - that live in a wooden box. But I have a few additional odd-size forstners that reside in a rack on the wall. Likewise, I have a set of large diameter Silver and Deming bits (1/2" - 1" with reduced diameter shanks) that also came in a wooden box.
I used plastic tubes with caps on the ends I have acquired from buying turning tools and my wife's bead supplies.
I label the outside with drill size and kits it is used for.
I store them in a larger metal index card box I got at work that was being tossed.
I have all my other twist drill in metal cases for number, letter and fractional sizes. Plus two complete sets of all three. I used to work as a machinist years ago so something I used daily.
Other wood bits that came in sets usually have their own boxes.
I also have assorted sizes in my tool boxes- both machinist and wood pattern maker ones.
You can always make a drill block to hold the ones you use for pens to save time hunting them down when you need them.
Greetings from Nebraska - I have a plastic compartment box where I store my pen making drills, reamers, and extra mandrel shafts and stuff. I put each drill bit in one of the square plastic tubes from PSI and add a label to all 4 sides for easy identification. It works for me. - Dave
I have several sets which came in there own cases. I also have a set which is all of the standard, letter, and metric bits for the pens kits that I make. I store those in a holder which was made by one of the members. I think it was by Hanau (username). He aslo made me a custom one for holding drill bits for the various taps and dies used in making kit less pens.
I used a filing cabinet with cardboard corrigations in the draws to stop em rattling. There are still 2 drawers full in it ! Then there’s the drill sets in dedicated boxes, then there’s the containers with bulk buys of certain sizes like David’s above . Sometimes I even right the sizes on the boxes.( not as often as I should I admit). Then there’s the ammo case with the taper shank drills set in wooden blocks. Then there’s the plastic tray of “ use these often so I’ll just keep them over there”.