I usually have a produce section in the top soil layer, this includes farming, brewing, cooking, butchering, and tanning. For my current fort, each room is 4x7 with two of the same workshops each, with a large multi-purpose storage area nearby. The farm is large enough for 4 5x2 fields, with a free space between each field and the walls. Seed storage is a 10x10 room dug beneath the farming area, with stairs leading to it between each feild near the wall. This floor is directly linked to my food stockpile and my drink stockpile.
The next layer is where all my workshops go, I use various layouts for this floor, depending on what idea I want to try. My current fort just has a row of 7x4 rooms with two workshops each, taking full advantage of quantum dumps for raw material storage between the workshops. The wood-crafting room is right across the hall from the carpentry for easy resource sharing, same with mason/stonecrafter and all the fuel using shops. The hall leads directly to A. the storage for my trade goods, that is in a semi-circle around my depot B. my bedroom floor and C. My dining floor.
The room floor consists of four wings of 3x3 rooms, 5 in each row 10 per wing. This is linked directly to my work floor and my dining floor.
My dining floor is the lowest floor. It has a middle room that can have 4 rows of tables, placed in the following pattern from front wall to back wall: Wall, space, space, chair, table, table, chair, space, space, chair, table, table, chair, space space. Where each "chair" "table" or "space" representing a row of 10 tiles of each, horizontal to the direction we were counting them off. The entrance of the dining hall is lined by a food stockpile on the left (roasts only, no exceptions) and a booze stockpile to the right.
The entrance is a large 20x10 entrance room that leads to hallways A. leading to the produce sector, this is on the same floor. B. leading to the depot C. leading to the work floor D. leading to the room floor. There is no hall leading to the dining floor, as this is where all non-military dwarves take shelter. All hallways are 10 tiles long and lined with traps, floodgates are at the entrance of each hallway.
Directly above the entrance room is a castle. This is where the barracks is, and where my nobles reside. It is 3 z-levels tall and is shaped like a castle, with circle towers containing the barracks of the normal military and town guard in the front two, and the royal guard in the back two. Sparring is done on the lowest level of the towers, sleeping on the third and shooting on the second placed at the corners of a rectangle. The nobles rooms are on the second and third floor, while the kings room takes up the entire first floor (of the central rectangle, not the towers). All nobles rooms can not be reached through the castle directly, there are paths that lead from the room floor into the castle interior.
There is a moat and a drawbridge before the castle, and the very front of the castle has a 5 tile long entrance of ramps into the entrance hall. The main entrance into the military section of the castle is two sets of double doors located on each of the front towers.
Note that every hallway is lined with traps, every exterior wall is two tiles thick, every hall is three tiles wide, every natural stone wall will be smoothed and engraved by my single legendary engraver, and every constructed wall in made of blocks of the best stone I have available, in my current fort I was lucky and had lots of obsidian.
Every dwarf gets a 3x3 burial chamber that is at least 5 z-levels under ground, these are arranged in wings similar to my room floor. At the entrance, on the surface, there is a 7x10 room, lined with pillars and statues, leading to the catacombs.
This is pretty much standard, but the way I lay out the rooms and floors can vary quite a bit once I hit on better ideas.
It has evolved from a single hallway, in the first z-level, lined with 5x5 rooms that were used for everything.
Edit: I would just like to point out that I always have 70 dwarves, and I forgot to mention there is a small hallway where I keep my cows, with two farmers workshops for milking and cheese-making. Each cow gets its own pen, I select the twelve best male and female breeders and each get a single tile room lining the hallway. Also, if I feel like it, a complete textile industry (with its own farm for textile-related plants) will be set up on the first floor.
I have also come into the habit of making exploration camps away from my main fort. These consist of a small barracks for the exploration-party troops, dorms for the miners, a small farm, a small brewery, and a single pair of cows. Also includes a planter, butcher, and milker/cheesemaker along with associated workshops. It's primary function is to explore the depths and deal with whatever threat lurks below. It also provides an armed escort for the caravan, since I always make sure to place it near the road the caravan takes. It comes complete with a big-red-level of self destruct in case something horrible is provoked. I consider the game to be played from here, the rest of the fort is just nice to have.