My forts are more or less designed to be dwarf-proof. I try to lay things out so that I don't have to forbid going outside during a siege (messes up my above-ground farms) or other things like that.
My workshops all have doors and a space for a cage trap inside the door. The door is for locking to cut access to a workshop for when a cat leaves a rotting corpse in there, and the trap space is just in case of failed moods - I usually don't bother to install the trap unless there's a moody dwarf working. The workshops go above or below a rather large open space designated with as many stockpiles as I need, with pairs of workshops stacked above/below each other with up/down stair access. My fueled workshops go below, because that's where the magma will go (well, it'll go one zlevel below that, anyway).
My workshops:
+----+ +----+
|....+---+....|
|.....DXD.....|
|....+---+....|
+----+ +----+
My refuse piles are all inside (so I don't lose bones to lazy haulers), I make use of the fact that miasma doesn't travel diagonally but dwarves do. No dwarf ever has to step into miasma to drop refuse in my dump, no matter how many things are rotting.
XXXXXXXXXXXXXXXX
X.X.X.X.X.X.X.X.
.X.X.X.X.X.X.X.X
................
X.X.X.X.X.X.X.X.
.X.X.X.X.X.X.X.X
XXXXXXXXXXXXXXXX
The refuse stockpiles go in the outer edge
I also like to use shafts cut all the way to the bottom level with access on all zlevels - I designate them as dump zones, and put an atom smasher at the bottom, with levers on all zlevels next to the access to the trash chute. If a chasm, bottomless pit, or underground river terminus is convenient, I'll use that instead of an atom smasher.
Housing tends to be uninspired - vast stacked blocks of 3x3 rooms with 2-wide hallways.
One thing that I do that I don't really see mentioned is I make separate rooms for the different quality/materials of weapons and armor. Long before I get my metal industry up and running, I have those rooms dug and designated. Basically, I set the stockpiles to only accept certain metals and qualities. This way if I want to equip my soldiers with poor-quality silver weapons for training, I just forbid all my weapons from the stocks menu and unforbid the 'training' room which contains my poor quality silver weapons. I can also use the mass designate tool to send all my bad quality gear back to the smelters - since all the bad-quality stuff is in it's own room. It gives me a lot of control over what my military dwarves use, without the problems that seems to plague many of the other forumgoers.
On that note, I try to avoid doing anything that requires me to remember that I forced a dwarf somewhere for me to do something with once they get there. Since dwarves tend to take forever to actually get there, my attention will have wandered off and the dwarf will likely die of thirst (or get really, really thirsty and hungry) before I remember about him and do what I was going to do originally. That's why I designed the auto-sorting rooms for my military gear, so that I didn't have to remember that I stationed them there so that would be the closest weapon, or whatever.
Strangely enough, I never really got comfortable using the manager. I overproduce raw materials, so that I can just keep the workshop on repeat and not have to worry about it. It's either repeat, or have several identical workshops next to each other so I can queue up 30 or 40 beds (or whatever) at once, just in 3 or 4 workshops. Consequently I have many, very large stockpile rooms. I've managed to completely fill up a 20x20 room with beds, barrels, and bins, and the only manual thing I had to do in that process once it was set up was keep designating those trees to be cut. I didn't notice I had that many of those until I noticed that the carpenters workshop was at max clutter.
I don't like to have any idlers, so if I see that I always have 2-3 idlers or more, I'll just start up another process on repeat, like sewing images or decorating with glass or something. I always have a few engravers smoothing and engraving everything (depending on terrain, I'll even do it outside).
Once the fort gets mature enough, I'll start sorting furniture by quality and uninstalling poorly made stuff and replacing them with better quality. The bad stuff gets dumped in the garbage chute and atom-smashed into oblivion. It takes a long time to completely replace all the tables and chairs in a large dining hall.
As part of this incremental upgrade process, I also remake all of my workshops with blocks, and later bars of precious metals.
My mega-projects aren't about giant towers, but making everything that my dwarves interact with be masterful with masterful decorations, if possible - this means doors, traps (including both the mechanisms and weapons/cages), bedroom sets, dining hall ... everything.