Thanks. Some quick remarks:
If you care about efficient fortress design, it's all about minimizing time spent walking and hauling, especially by your highly skilled dwarves. (I'm ignoring defensibility here, this is best taken care of at the entry points, but I guess good compartmentalization can save your dwarven behind when things go really wrong. )
Since carrying a heavy rock up 1 flight of stairs takes a dwarf as much time as carrying it one tile accross, z-levels are the key to efficiency. I normally place related industries in a room with some stairs leading down to the raw good stockpile and up to the finished good stockpile(s). That way, the artisans generally only have to haul <10 tiles (from pile to stair and from stair to workshop). You can e.g. have 1 tile space between workshops and have a staircase at every interception like so:
workshop level (z=0) storage levels (z=-1, z=+1)
WWW.WWW.WWW ===========
WWW.WWW.WWW ===========
WWW.WWW.WWW ===========
...X...X... ===X===X===
WWW.WWW.WWW ===========
WWW.WWW.WWW ===========
WWW.WWW.WWW ===========
...X...X... ===X===X===
WWW.WWW.WWW ===========
WWW.WWW.WWW ===========
WWW.WWW.WWW ===========
Of course, you can make this as small or large as you want. I cluster workshops with the same material together (e.g. ason, craftdwarf, mechanic) or if input of one is output of the other (forge+smelter, loom+clothier). You can also do a five story layout (ore > smelter > bars > forge > weapons) but that's too much fuss to me, and doesn't work for magma forges anyway.
Same goes for bedrooms. If you spread them accross z levels total travel time is much shorter. In theory you could make sure masons live near the masonry shop etc, but that's too much work for my taste. See 'dwarven apartments' for a good design.
It is also a good idea to spread little booze stockpiles around and place some nice statues or furniture around them. Dwarves never consume drink in the dining hall, so you might as well minimize travel time and maximize good thoughts.
In terms of labor management, I usually have a large pool of "peasants" doing all labour without quality levels (hauling, processing/milling, smelting, architecture, brewing etc.). Skilled dwarves only do one thing plus hauling, and experts (especially smiths and CMD) do only that thing. You can go a bit further if you have e.g. a legendary mason, and set him/her to masonry only and profile the furniture workshop to only allow him/her, and use the lesser masons for blocks.