This is my current fort and, while I am experimenting with a lot of magma functionality most of this fort, is typical for me.
Level 1 Walled and covered in flatland with overcomplicated entrance'o'doom through the mountain including weapon traps, isolation bridges, two separate magma flooding areas and barracks for two squads set to train all the time.
Level 2 (the first one completely underground) Expansive farming/brewing/cooking/butchering/tanning/dying/plant-processing operation with my main stone block stockpile. Also, my first mass grave area.
Level 3 Blockmakers and large furniture stockpile centered around main stairway. One of my legendary dining rooms, my animal stockpile, and my second mass grave area.
Level 4 (this one is a little different because I don't usually embark on a volcano) Here I have a mega-forge complex with housing and legendary dining room (in which i keep my smelters, glass-makers, and metalsmiths burrowed). On this level we find the danger room, and crappy weapon/armor stockpile for training. There is also a barracks and a third legendary dining room. You can also see a large sand bag stockpile, as well as two (of the three) large magma safe pump component stockpile and a line of work out equipment (screw pumps). Surrounding the stairwell is an odd assortment of workshops so I don't have to bother making a place for a mooded dwarf to work.
Level 5 is a typical housing/storage layer.
Level 6 is a typical legendary craftsdwarf workshop area. I like to keep my legendary craftsdwarves burrowed so I can control what material they use to make stuff. There are small stockpiles for every type of good I will have them produce. In this area I have separate stockpiles for each of the stone crafts (amulets in one, rings in one, etc) so an unfortunate mandate doesn't take out my entire stock of trade goods.
Level 7 Another housing level with a barracks yet to be designated and my cotton candy weapon and armor stockpiles.
Level 8 is a housing level with a large furniture stockpile (I make bins to train up my blacksmiths) and two noble/mayor housing complexes with installed over complicated drown, drain and dry functionality.
Level 9 is my legendary mason's burrow. He cranks out all of my gold furniture.
Level 10 is housing, and my leather and clothes making industries.
Level 11 holds my gem industry and third magma safe pump component stockpile. To the right is the access/drain for the entry pit/magma bath. The magma drains into reservoirs that go down an additional 10 levels are then pumped back up to magma holding tanks a few dozen z levels above.
I welcome any advice.