I tend to build my fort around the entrance. I mean, first of all, I have two entrances. One entrance is a single tile wide, long winding path leading to the fortress itself, the other is a short three tile wide path leading to the Trade Depot.
If the ground is flat, the Trade Entrance is two levels down and has ramps separated by at least two tiles.
I dig until I hit stone. This level is ignored, except for having two branches dug. One leads to a stair case leading to the bedrooms. The other leads to the exploratory shafts.
The Bedrooms are two levels down from the stairwell level, and have stairs leading back UP to the Farms, which are separated from the main entrance. The stairs are also near the kitchens. Bedrooms themselves are 3x3, except for nobles and administrators, who have more complex set ups. Generally 5x5's lined with statues for the Nobles, and sets of three 3x3's for the administrative staff who need offices and dining rooms.
The Dining Room is right beside the kitchens. Directly above the Kitchens is the food stockpile, which is directly below the butcher shops. Farms, and livestock are immediately above the Butcher's Shops. Tallow/Soap is located near the Butcher's Shops.
Down four levels form the bedrooms, using the down side of the farm stairs is the workshop levels. This consists of three floors, built directly below the trade depot. The top floor is reserved for Furniture/Finished Goods stockpiles. The next floor contains 3x3 work shops, for anything that needs bigger, those are built a little ways off. Each room has a door, that can be locked in case of strange mood fun. Beneath each workshop is a stockpile in a 3x3 room, containing raw materials for the workshop above. Access to these is provided by a separate door, which must also be closed in case of strange mood fun.
This allows haulers to get into dump off fresh stocks without disrupting the working dwarf. Three levels lower, is where Magma Forges are housed. These forges have an access way which can be sealed from the main stairs up by Magma Sensitive Pressure Plates. Stockpiles are arranged one level higher than the forges, and have an access stair opposite the Magma Proof Access Way, so Magma can't escape up through the forges. The level below the forges is constructed identically to the level above, and filled via the central chamber. For best use, the floor should be replaced with hatches and each room sealed with Magma safe floodgates to ensure that further rooms can be dug out safely should they be needed.
I usually dig a room not far away, on the same level through the same access way and convert it into a water reactor if magma is far away. This allows me to provide power not vulnerable to the surface and also maintain the integrity of the magma forge power supply. Plus if I have an 'accident', I'm not loosing main fortress power, nor do I have a problem with enemies disrupting my ability to manufacture metals.