Funny You Should Ask
Funny you should ask about this, I just conjured this solution up to the same problem you're facing, and there is not much in my shop that I am prouder of at the moment (I am SUCH a dork).
I had a lot of different sizes, with only one or two of each. Lots of 6" bits plus lots of threaded ones in short, medium, and long. I wanted easy access, expandability, and it had to be cheap.
The shelves I made from scrap lumber, and I bought 100 boxes from
PaperMart online.
They're 6-1/2 X 1-3/8 X 7/8 WHITE SWIRL SILVERWARE BOX, #451061, $33.00 CASE + Freight $8.69. They come with foam in them (toss) and the tops are a bit deeper than the bottoms. I still have probably 30 tops and 100 bottoms if you'd like some, contact me.
The top shelves have some sizing guides, unibits, and other packaged sets. You can probably see I've got multiple boxes for 1/4". All the bits, as well as threaded bits, countersinks, reamers, and deburrers fit great, but when they don't, or when you want to keep new from used, or reamers separate, just add a box. Also, as I add new sizes, there's plenty of room to grow.
Hope this helps.
George