Thought I would share (and welcome criticism on) the central stockpile design I use for many of my forts. Should be noted here that this is still DF2012, Vanilla with the Defense mod, Soundsense/LNP/Therapist running, and Cartilage modified to count as a [SHELL].
It is a very simple design, though some mine-cart knowledge is required. I developed it because I am slightly OCD when it comes to what stone my masons and stonecrafters use in their work; having convenient stockpiles to link to them that are stuffed with that one stone I want is great.
Take a large room, plop a big-ish custom stockpile in the middle. You can alternatively plop down many little ones, and give each wheelbarrows to speed up collection.
Along the edges of the stockpile (or group of stockpiles), place outwardly-dumping track stops. Then, place a single 1x1 custom stockpile in the tile each track stop will dump to, and make it so it only takes from links (and do not set any links).
At this point, you can do what you want with it. I generally start with organizing my stone and ore, though you can easily have it organize furniture. In my case, I will set the big stockpile to only accept the type of stone I have the most of, and off my dozens of idling dwarfs will run to stockpile it. I then setup a route, named appropriately (like Granite) and put a single stop on top of any of the Track Stop (this will put the mine-cart there). Delete the preloaded Stop settings, and simply tell it to take from the big stockpile (or aaaaall the little ones), and set the desired item to whatever you want (Granite, in my case). Assign a mine cart to the route, and voila. Your minions will now not only take the desired item to the stockpile, but also load it directly into the mine-cart, which, as it is sitting on a track stop, immediately dumps it into the 1x1 stockpile.
In most of my forts, I have a small version of these for Refuse (dumps an entire refuse stockpile onto a single 'Inside, light' tile to prevent miasma), Wood (goodbye massive wood stockpiles), and Stone (automatic stone organization once setup). If I ever get a metal industry setup, I'll have another for that (Coal, Bars, etc).
It's very nice for stone gathering as, once you have it set up and are caught up on gathering the stone you dug out to date, the stockpile will keep up with it forever. Dig out a new room or mining new ore? All that stuff with be automatically tagged, picked up, and organized.
Here are a series of gifs that show the process; in them, its barely a year into the fort's lifetime, and I have just begun organizing the stone scattered around the fort.
Stockpile Overview
Setting the Collection Stockpile
Setting the Quantum Stockpile
Setting up the Route
Result
And in case the gifs do not load here (still new to posting), here's the Imgur gallery with all of them: