I actually use a combination of the first three methods in the poll. But the system would only allow one choice.
Long ago, I "stole" some
empty set boxes so have several "sets". They are divided up based on several systems. First off is Metric, Fractional, and "special" threads such as ACME and "unusual" threads such as 1/2-40. FWIW, I used to do jobs that involved 40 TPI, a loonnngggg time ago. Each of these has their own cases. I have a set of Craftsman taps, Nr6 to 1/2 inch in the original case. The others are built up, over time. Sorted by size, sub sorted by TPI.
Then there are the smaller sizes, Nr4 and smaller. I took (nominal) 1/4 Plexi' and glued up a stand. It contains Nr 4 down to 3/0-120 taps and the appropriate tap and clearance drills. Metric equivilents have a cute little plastic case.
And lastly, there are many sizes that are duplicated because I use them on a regular basis. If something happens at 3AM Saturday I don't want to wait until Monday to order a replacement. These are kept in drawers in envelopes, essentially as they are acquired. There are also a few oddities such as 1-1/2x8 and 1-1/4 IPT that are kept the same way because of their rarity of usage.
Taps, excepting pipe and the one large machine size, only get as large as 3/4 inch. Threading dies are kept with the taps for the most part. With the same systems. Tap drills only get as large as 1/2 inch. The drills, other than the small tap sizes, are kept in indeces. Spares are in envelopes in deep storage, same as the spare taps.
My systems will probably be useless to the average person. The extent of my tap sizes is rather large because anything I used at work was usually duplicated in my personal shop. Usually
at my expense, not my employers'. Add to that the small sizes used in my model building and (ex)motorcycle maintenance and the sets are extensive. ++
Edit++To acknowledge the above post, I have magnifiers at several locations in the shop as well as a portable glass in my pocket. As well as my eyeglasses.
Bill Hudson