This is 3D printing rather than milling but thought it still might interest some. I was getting sick of my giant pile of endmill cases, which made it difficult to find what I needed, so I 3D-printed some little trays to hold them.
I turned this pile of boxes (though they weren’t stored in this bag):
Into this neat little pile of trays:
Very nice!
I can’t quite bring myself to divorce the tool from the (labeled) storage tube (and need to work up a way to label the blank tubes some come in and to source tubes in a way which will satisfy my OCD.
I’ve also been thinking I should just begin directly entering usage notes onto the packaging in some way — maybe a color-coded system of dots — can’t quite be rigorous enough to use a notebook.
My thinking right now is a two-tiered system:
But after watching CGPGrey’s latest video, I have to say I’m tempted to redo these with hexagons… I’m thinking basically honeycomb with the back of endmills sticking out of it. That should make it easier to access lots of them too.
My thing is, I want at least 2 of each tool – one for roughing passes, a second only for finishing — it just gets more complex from there.
Your solution of “dots” is not permanent nor readily extensible. However, a solution is sort of right in front of your nose … XYZ coordinates. 
Which, if used, sort of distances the solution from the infamous “hexagon is bestagon” theory.
The regularity of circles (holes) and squares (gaps between grids) seems to fit XYZ so much better.
I like it. Maybe I would make a grove at the bottom of the “row” across all bits to make it easier to take them out (e.g. space for my big fingers to go) but other than that it looks perfect
Thanks for that suggestion! How to resolve that problem has been bugging me since I finished this. I’ve been using tweezers (annoying but better than hunting for the right container then grabbing pliers to separate the endmill from the cap) but a simple 10-20mm slot at the bottom of the row would be perfect!
But you could have milled this out of a solid piece of plastic and and made a pile of chips 
Great job and inspires me to do something about a similar pile of bits boxes.
How do you remove the endmill from the tray?
EDIT: Read further… Saw the tweezers post.
To make them easier to remove from the tray you could also make the slots deeper at the plain ends. To remove the cutter you could push the end down, tipping it up so that you could get your fingers around it and easily remove it. Hopefully that description makes sense.
Hmm, I really like that one. I was thinking of adding some kind of lever underneath the endmill at one point but your idea is so much cleaner. It also avoids having to fit your fingers around the endmill, you just need to be able to press on it, which should be easy even with sausage fingers like mine.
For those looking for inspiration, the First Community Challenge was for bit storage. There are some really good ideas and pictures to get you started.
Maybe that’s where I originally saw the idea and it popped up in my subconscious mind. 
Made this for my bit storage, 1/4 and 1/8 inch, plus trays for miscellaneous pieces. Larger bits like surfacing/fly cutters go vertical. I have been using it for over a year and haven’t had any issues with moisture or oxidation etc. I believe I sealed the wood with polycrylic.
I use a laser cutter to engrave and cut acrylic inserts with the bit details. can store up to 10 of a single type of bit or split the storage area into two.
I like your trays but for me they take up too much room. I bought this plastic case at Harbor Freight. I like to keep the bits in thier protective case and I make marks on the package when the bit is used. Wish I had the room for your great looking trays. This pic is from a year ago and the box is fuller now.
The trays could easily be altered to fit into your box. The slots look ~40mm wide, which should be enough for a tray of 6 or so endmills at least.
whats the plant on the right?
Those are two crepe mertles that need to be planted.
