My layout uses a simple basic design, but the components of it are module, so I can move them wherever.
At the center of my fortress is the meeting zone. Usually some sort of multi level great hall, with engraved stone pillars. Think Moria. Its also not always square in shape. Often times it really is a hall, stretching from one side of the map to the other. The entire thing is designated as meeting zones so all of my idle dwarves hang out chatting in the hall, making it suitably epic looking.
Off of the central great hall are the work areas. These are:
Smithy, contains all smelters, glass workshops, and other metal related things. Magma powered of course. Storage for bars/blocks, weapons, and armor is all on a Z level above or below the workshops.
Factory, all other workshops, group together in the same large room in alcoves, storage for cloth, leather, finished goods, and gems are stored on the next Z level(s) as appropriate.
Tavern, contains my dining hall, food storage, and food workshops, with farms located a short distance from the dining hall preferably on the same footprint on a different Z level. Primary booze stockpile is within the tavern, but there are numerous other booze stockpiles strategically located around the fortress.
Offices, large, customized rooms for nobles or other important dwarves. They get their own fortified wing, one that can be shut off from the rest of the fortress and defended in case of invasion...or if the regular dwarves just get tired of the nobles.
General housing, large blocks of 3x3 rooms for housing for ordinary dwarves.
Refuse, contained in several very large stockpiles usually located in an out of the way section of the fortress, such as stacked vertically in one corner of the map on my current fort. These stockpiles contain refuse, as well as stockpiles for furniture, unused animal traps, and wood. Its the stuff I don't use frequently that can mostly just sit around while I decide what to do with it. Allowing the same stockpile to accept refuse, corpses, furniture, traps, and wood gives me flexible storage options. At the very least I will have 4 maximum size stockpiles of this type, but with engraved natural stone pillars in the middle for support.