Edit 8/15:Quantum industrial complex in practice in my current fortress:
http://mkv25.net/dfma/poi-29675-quantumindustrialcomplexHere is a design to compress your entire industrial output and storage into a small and compact industrial complex all located on the same level. Note that in this design I'm using 3 workshops of each type. You do not need to use as many workshops, or you could use more, so this design can be scaled up or down at will.
This design heavily abuses quantum stockpiling from mine carts. When a mine cart hits a track stop that has dumping enabled, all items will be dropped to the direction the stop is programmed to dump items. This is completely safe and will harm no dwarves. No mine carts are ever out of control as all mine carts are guided. No pushing or riding, only guiding allowed. You will not have any fatalities due to mine carts with this factory complex.
Another perk of this factory complex is that it requires zero wood. You don't need to make a single bin. Due to the quantum nature of storage and the new hauling behavior involving bins, using bins will significantly reduce efficiency. Not using bins actually improves efficiency.
And now onto the design itself. Behold, my dabbling skills in MS Paint!
Here is the key for the tiles:
Black = walls
Brown = workshop
Green = stockpile
Yellow = minecart tracks
Blue = booze
(Apologies for the poor quality for the flowchart. I find that MS Paint is actually very good for drawing thing on a pixel basic, which lines up to a per tile construction in DF. Its very poor for flowcharts.)
Don't allow any stockpiles to use bins to make this work. No bins! Nope. You don't need them. The central stockpile acts as the sorting depot. It accepts nearly every type of item in the fortress.
Items from the main sorting stockpile are divided up into multiple different 1x1 quantum stockpiles using minecarts. The quantum stockpiles are next to relevant workshops to boost efficiency.
You will get a lot of haulers doing short hauling jobs, moving things a few steps each time. Once a cart is full the cart will be guided to its stop, where it will dump the items next to the stockpile that uses those item types.
The main sorting stockpile will of course require input in order to function. In order to supply it bones and skulls for crafting as well as stone and ore build a mine cart route and track from your butchery workshops (likely located near your kitchens and dining hall) and from your quarry area (including obsidian mine). These mine carts can be dumped right into the sorting stockpile still using the quantum method, and then reloaded into carts on other destinations.
To further separate out what items are stored where, I build two stockpiles that store finished goods, weapons, and armor. The stockpile on the side of the forges, jeweler, and crafts workshops accepts only masterwork and artifact grade items. These items are decorated continually so they menace with spikes of bling. The stockpile on the smelter side accepts low quality finished goods, weapons, and armor. Periodically just mass designate that entire 1x1 square for melting, and put the smelter to work melting down the goblinite or low quality rejects from your forges should any weapons or armor fail to live up to expectations.
Not addressed in this stockpile is the manufacture of clothing items. I suggest creating a small area that includes pig tail farm, 1 farmer workshop, 2 looms, and 1 clothier workshop. Also include a stockpile for pig tail plants and pig tail seeds.
Then create an additional stockpile that accepts clothing items only. Have that same stockpile also act as a refuse stockpile which accepts no types of refuse. This means no refuse will be hauled to the stockpile, but any clothing items on it will rot away to nothing. Allow the clothing/refuse stockpile to use bins. Clothing will be continually produced and recycled in this room. Excess clothes will just go away on their own with no intervention needed. Dwarves who need new clothes will pick it up before it has a chance to rot. Clothes not needed will rot away over a period of months.