Follow up at the 2/3 mark.
I think I'm going to really, really like this system. I didn't really realize how limiting it was having nibs in recesses in one larger tray. I keep running into so many that are out of order because I got them later and didn't have room to shuffle all of the other pens around. With each one in a separate box it's so easy to add a new one.
The challenges I'm encountering are two fold. One, I realize I have more different types than I thought which I shoved together because there wasn't room and it was easier to put them together rather than shift everything around. And that's not including the realization that I had thrown the Hunt, C.H.Hunt and C.Howard.Hunt nibs all together. If I'm going to sort them, then I might as well sort them. This led to the discovery of the differences between Spencerian nibs with "England" or "Made in England" on them vs. those which have nothing. It's the same as with the Spencerian #1's.
The other challenge is that I hadn't realized how many pens I had just sorted into bags waiting for more room in my current system. I now have purchased 800 small boxes so that I should have a fair number left over for new acquisitions (and some nibs take up two are even three boxes if I have a lot of the big ones), and I had to get another set of drawers, which makes four three-drawer sets.
This leads to an actual third challenge. My pen collection is going to be a lot more visible.
Up 'till now I had them scattered in boxes here, and boxes there. Now with a growing stack of drawers it's much harder to hide just how many I have. I don't know how many my wife thinks I have, but I'm pretty sure it isn't this many.
As soon as I finish transferring them all into boxes, then I'm going to sort them into final order (leaving gaps in each drawer) and then I'm going to go through and compare and count them against my spreadsheet inventory. That should be interesting, and quite a job.
And speaking of the gaps in each drawer left for growth, I've found a good way of dealing with those. The boxes I bought each comes with a small square of polyester "jeweler's cotton" on the inside. I wasn't sure what to do with all of this fluff (thoughts of pillows came to mind) but then I had the ideal of filling these open spots in each drawer with this padding. It works well as the whole purpose is just to keep the other boxes from falling over, and as I add a box here and there the padding compresses so I don't actually need to adjust it unless I add more than a couple of boxes.
So, that's my impression to this point. After I get it finally organized I'll take pictures. This is probably overkill if you have a few dozen types, but once you're getting close to 100 I'd recommend something like what I'm doing.