I realized that my storage rooms were growing to incredible size to try and fit everything, and that it was getting so big as to be a pain in the ass to build. So I re-did it from the ground up and here is what I came up with. The colors are left over from previous rooms and don't mean anything.

The new storage room is 36x23, or 36x20 if you shrink the main hall and remove the end blocks.

The chests containing multiple items are capitalized and the list of what is inside is listed beside the diagram of the room. 1-9 are the columns of the chest.

8 rooms, mentally I've labelled them Dirt, Mining, Stone, Plants, Redstone, Items, Wool, and Explosives.

Dirt (pink)

Dirt, grass, sand, gravel, and other top of the world coverings and their by-products.

Ores (magenta)

Stuff you mine that has value (in theory). Clay blocks and bricks are in here too. Raw ores (mined via silk touch) are stored in 1 crate.

Stone (purple)

Stone, stone by-products, and nether stuff. m cobble = mossy cobble.

Plants (orange)

Plant stuff and house stuff like ender chests and furnaces.

Redstone (cyan)

Redstone stuff, rails, and torches.

Items (dark green)

Items. Why so many chests? Because enchanting eats up tools.

Wool (lime)

Wool, and dyes. And mob drops.

Explosives (red)

Explosives, which I don't really ever use.

All in all, I think this system is a nice balance of simplicity and size and functionality.