I put the vast majority of my fortress on the first four below-ground z-levels. Farming, food production and related industries, dining, and food storage go on the first layer, because the soil makes it easy to set up farms and to dig out more storage space. Almost all of the other workshops and industries go in the layer below that, assuming it's mostly stone. I also put my primary stockpiles on this level, which take the products from the workshops. Below (or above, depending on the arrangement of stone/soil) the workshops go my input stockpiles, which hold the raw materials for the workshops directly above them. I also put some overflow stockpiles on this level. Below that I put the bedrooms, jails, and offices.
All the levels (except the bedroom level) share a general floorplan, with a central 3x3 staircase between them. I extend a 3-wide hallway in each cardinal direction from this staircase, and build square rooms of various sizes to hold the workshops/stockpiles. I generally make branching hallways to separate different industries, with a hallway for metalworking, one for masonry, etc. I build four workshops to a 7x7 or 9x9 room, with a stairway in the middle leading to the input stockpile.
For my bedrooms, I dig a 1x4 room for each dwarf, and give each room its own door, bed, chest/coffer, and cabinet. I keep the 3-wide hallways, but dig them parallel to each other, rather than perpendicular.
My hospital goes on the first level below ground, as close to the river as I can get it. I dig a large cistern under it, fill it from the river, and build wells inside the hospital.
Depending on the terrain, my aboveground structures vary wildly. I usually wall off a small area, with a double-drawbridge-airlock system, then put my depot there. The first drawbridge allows access from the surface to the depot, and the second allows access from the depot to the fortress. I also put another wall around an area to use as a refuse stockpile, because I don't really like putting them underground.