You are describing what I basically do Hittman; and I just had to revamp my "system" (or lack thereof

) last week. My latest flavoring order/shipment has pushed me over 180 different flavors on hand and over 210 if you count the ones still remaining on my
current wishlist. Sadly it has outgrown my previous method using the plastic drawers that Slots was describing. I was never a huge fan of those for all my small 8ml. testers (which is primarily what I use) because the bottoms of the drawers are not completely flat, so the tiny bottles had a tendency to shift and tilt, and they are semi-translucent so they are not great at keeping the light out. But they are great for all the rest of my gear.

So I went on a mission last week to find something that would work for me. After going to Depot, Lowes, Harbor Freight, and Walmart, I found myself at Hobby Lobby. First I looked at their plastics but nothing wowed me (I really was looking for something with squared, as opposed to rounded, corners so the small bottles would have solid contact). So then I started wandering through the store for ideas. I found some serving trays that really intrigued me; squared low sides, nice and rigid, and tons of room. they don't have a lid but I intended to put it in a linen closet when I wasn't mixing so that wasn't a deal breaker. Actually I could actually put
all of my mixing liquids (other than the refrigerated ones) on it regardless of size and still have copious amounts of room. The only real drawbacks to me were I was afraid it might be too big (read "unwieldy," "heavy," "space-hog," and wouldn't promote stacking), and expensive. My being a cheap old geezer; price was it's greatest offense at about $20. So I continued to look around.
That's when I stumbled upon these:
12" x 12" Photo Storage Box | Hobby Lobby | 190470
I paid the full $7 but I see they are now half price. The dimensions are listed as 12" x 12" but mine measures 12 5/8" x 12 5/8" x3" deep
internally. The slip-over lid has a 1 1/4" lip so it will accommodate bottles a taller than 3"
The Photo Box and a piece of foam board:
http://www.hobbylobby.com/Art-Supplies/Canvas-Surfaces/Foam-Board/White-20"-x-30"-Foam-Board/p/101651
and I was ready to go to work.
I cut the foam board into 1 3/4" strips to make row dividers and cut them at the full 12 5/8" length to make sure they were snug and stayed in place on their own without having to glue or tape them into position. That way I can move, remove later if my needs change.
That has left me with this: