I usually give each workshop its own storage area. Usually a 3X6 area if its something like a carpenter's shop, or a mason's workshop. and a 3x4 area if the shop can stacks its resources, like a jewler's shop.
If i have a magma pipe, or a magma pool, i'll channel out an area, place a fortification inside, and then place all my smelters, and forges along with this channel, with a large area mined out to store all of the ore and bars. If there's not, i'll still mine out a large area, but use this to store wood, which is made into coal, which is stored next to the ore, and then both are used inside of a smelter. The bars have their own stockpile, and coal is then used in combination with bars to produce goods.
For the stockpile, there is usually a large stock pile for all ore, with smaller seperate stockpiles for say, copper (or malachite, which is the same thing) and cassiterite for bronze making, or a seperate stock pile for gold. Teh large one will hold anything else.
AS for the food industry, it should be located by the farm area, but with each workshop separated much like a the crafting shops. I will place the stockpile for all dwarven seeds by the farms, since dwarves never carry more than one seed for planting. A large stock pile, say 11x11 will contain any excess food your dwarves may have at any given time, as well as an extra area simply for extra barrels. The smaller stockpiles with the shops are used to contain only what the shop needs, and minimize walking distance.
As for my Depot, I move that indoors as soon as possible, usually behind a long tunnel with at least one 90 degree bend. This will prevent any enemy from shooting down the hallway, and hitting the traders as they sit at the trade depot. At the 90 degree bend, i will station a balista unit. so it can fire out in the outside. if there's another bend, i'll station another, but only if the tunnel itself is more than 150 tiles. Anything else is simply a waste, because the ballista crewmen will immediately run as soon as the enemy rounds the corner.
The dining area is massive, enough for several dozen dwarfs, with statues lining the wall. If i have enough zoo animals, i'll place a caged animal in between each row of tables. As for the size of the room, it depends on the material its in. Rooms made out of soil can't be smoothed, so they need to be made larger, quicker. For these rooms, i usually make them 13 spaces wide by 20 long at first: 1 space along each wall, (2 total) a walking space (2 for each statue) and two sets of tables (1 chair, table table, chair, walking space (or space for animals), chair table, table, chair), a total of 9 spaces, all of which add up to 13 There will be two or 3 entrance doors, one for each walkway. Prepared food will be in its own stockpile, along with booze. Usually there's an extra 13x2 space dug out at the bottom, just for the food and drink. This room will also function as my meeting hall.
There's also a public tomb, usually 3x5 or so at the beginning, where i can put coffins on wither side of a walkway.
after i've gotten a few veins mined out and my blacksmiths get to work, i'll get about mining out rooms. a common sleeping area, usually following the "3 by X" rule, is still used for any immigrants that pop in. Personal rooms are 3X4, and consist of a bed, coffer (or chest as its known, but only if its made out of something other than stone) door, table chair, armor rack and weapon rack (through these are for decoration only)
As for the general layout, the noise from the workshops will create an unhappy thought, so i make the barracks and offices 4 levels below the work shop area. The work area's are either placed directly above, or close to the depot itself, so you can transport more wares to said depot during the time limit, or there is a large warehouse area located next to the depot itself. you'll still need a large amount of dwarves set only to haul for this to work, (about 10 or so.) depending on how far it is. ) as dwarves have a tendency to do everything under the sun before they do what the NEED to be doing.
There will be a large refuse stockpile (well, small when the game begins) located in the rough center around my fortress. this way, dwarves can dump whatever they need to quickly.
my barracks is an 11x11 (you can use the shift key to quickly make a room like this. it skips ahead 10 tiles as you're selecting the dig area. and right by the depot. any enemy comes in, and they can quickly head to the bend in the entrance hallway. They can quickly ambush anyone who comes along, and arrow goblins and marksmen cant' get a good shot until my champions are right on them.