I got two chests for wood*, two for various stones, two for dirt**, a chest for mob drops, a chest for food, a chest for "organic***," and a chest for misc****. I keep all the "loot*****" items in chests in a hidden room. No idea why I bothered to hide them, considering I never play with anyone... Anyways, I also have a trash system, as any builder should have. You know the setup, a block of magma for throwing trash into. Usually busted old skeleton bows, shitty old armor and tools dropped by zombies, and rotten flesh. Coal is kept off site at the "smoothing station."
I keep a vanilla world where I put all the vanilla structures I really like. It's the third one I've gone through, seeing as major updates (1.8.

break the living shit out of my saves.
* Saplings included
** Dirt, grassy dirt, sand, podzol, gravel, hellstone, soulsand
*** seeds, flowers, grass, other plants
**** tools, glass, fences, ladders, lights, doors, furniture, half blocks/stair blocks
***** Gold, diamonds, iron, gunpowder, redstone, books, emeralds, lapis lazuli, TNT, enchanted weapons/armor, horse armor, name tags, slime balls